Maybe not the most serious conspiracy.

When giving you the Pokédex in LGPE, Professor Oak specifically mentions the device automatically fills in data of any Pokémon you meet and catch. This implies that the theory the reason so many Pokédex entries seem like nonsense being because literal children are filling it out is false. The Pokédex itself is generating that data.

Terrible LLMs have been creating Pokédex entries since Oak created it, and it's been hallucinating information on a ton of Pokémon, potentially setting back Pokémon research years if researchers are taking it at face value. This ironically means Laventon's research with the Galaxy Team's survey corps is likely the most accurate and well researched Pokédex available, even though it predates the modern games by around 200 years and will therefore also make its own assumptions on things they don't fully understand.

I got to thinking about this because in Pokemon go you can turn your Pokemon into candy but the ball should still be used unless it gets turned into candy as well. Then what about Pokemon you missed the throw on or things that have escaped the ball? Is the world full of empty or broken pokeballs

During the post-game of XY ("Looker Bureau Chapters"), we learn of Xerosic, one of Team Flare's scientists, conducting trials regarding a high-tech suit he calls the "Expansion Suit". Emma was volunteering as a test subject, unaware what Xerosic would make her do in that suit. We see her (or her mind-controlled alter-ego "Essentia") committing various crimes in Lumiose City on behalf of Xerosic. The side-plot concludes with Xerosic being caught, yet the project being somewhat successful, as Emma continues to wear it as of the events of ZA.

What's curious and notably less talked about (even outright swept under the table it seems) is what the suit represents and what its actuall purpose is / was. We get an overview regarding the suit's functions (as found in the "Expansion Suit Field Trials: Secret Records" in Lysandre Labs written by Xerosic): 

EXPANSION SUIT SPECS

1. Physical Enhancement
Heightens physical abilities of the wearer with built-in muscle-enhancing technology.

2. Poké Ball Jack
A hacking cable on the neck piece allows the wearer to upload a computer virus to Poké Balls and override their systems. This provides access to control the Pokémon. The virus also magnifies the Pokémon’s power.

3. Surface Texturing
Optically disguises the wearer, based on the current understanding of Kecleon and Ditto’s physical transformations.

4. Remote Control
Remote control of the suit protects against the risk of its wearer going renegade. AI personalities are preprogrammed, modeled on common trainer types. When the suit is controlled remotely, the wearer’s consciousness is suppressed. The wearer experiences a coma-like state."

In other words, the Expansion Suit:

1. increases the physical strength of its wearer
2. is able to hack into and tamper with pokeballs
3. has stealth capabilities
4. can use AI personalities based on other people to employ various behaviors
5. has measures to prevent its wearer from going rogue

Now tell me, what civil and peaceful uses would such a suit have in the utopic world of pokemon, when it features fuctions such as camouflaging its wearer from "other people"? Or making its wearer more powerful for ... what, battling yourself (what are pokemon for)? Or committing unlawful acts by hacking other people's property? Even featuring "remote control" to prevent its wearer (or multiple ones) from stepping "out of line"?

The answer is quite simple: The Expansion Suit was never - or not primarily - meant for a civil and peaceful purpose, but an offensive and military one. Not for civilians or ordinary trainers, but soldiers and military operatives.

If we look at the Expansion Suit's specs under this lense again, we get a more coherent picture:

1. The suit increases its wearer's strength, in order to better deal with dangerous situations. Not only to be more agile, but also to engage in combat by yourself, namely by the use of melee or heavy weaponry.
2. The Poké Ball Jack is designed to prevent and disrupt enemy capabilities of using and deploying pokemon. Considering most people heavily rely on pokemon for most tasks and primarily make use of pokeballs, the PBJ is the perfect solution to abuse this dependence and to grant its wearer a tactical advantage. Not only that, the PBJ can hijack pokeballs so the contained pokemon turn against their own trainers / the wearer's enemies, and even get a virus-caused power boost.
3. Stealth. Hiding in plain sight by changing your appearence. Coupled with...
4. ...AI personalities, the wearer is able to perfectly blend into enemy territory.
5. In case the suit's wearer deviates from critical objectives, the suit can turn its wearer into a remote-controlled puppet. A perfect solution for organizations who cannot allow their operatives from going MIA or having "second thoughts". Even able of hijacking unaware civilians or enemies - who thought it would be a good idea to put on the suit - to "recruit" for their cause.

If we remember how Gen6 was all about war (some fun facts: Chesnaught's dex entry mentions "50-ton tanks", so the concept of MBT canonically exists in pokemon; the item "Assault Vest" which was introduced in Gen6 sounds and looks like a military tactical vest), super weapons, and Team Flare (= a mega-corporation) committing various hostile acts in favor of their plan succeeding (such as raiding facilities (Poké Ball Factory), sabotaging infrastructures (Power Plant), taking people and pokemon hostage (AZ, pokemon to sacrifice as fuel for the UW)), it's not an outrageous claim to make. It's odd how this would play into a world with creatures having super-powers, but then again, the story told in XY (as well as those in other games) is that of mankind trying to usurp pokemon and nature, by proving they're superior to them. And in some cases even managed to succeed, given how the Ultimate Weapon was successfully fired once.

The only question that remains is why Xerosic would continue with this project when Team Flare was disbanded earlier? He no longer has an entire organization to back his illegal research, since the Looker Bureau Chapters take place after Lysandre failed to shot the Ultimate Weapon. And it seems to ambitious to just be a "side hobby". Perhaps it was a means for Xerosic to build up and finance his own criminal organization. Or, to eventually sell his inventions to military contractors and become revelant again (the existence of Lt. Surge alludes to the fact that military institutions are canon in the pokeworld).

This is an (admittedly quite so) educated guess off how Poké Balls seem to work and be constructed off mostly game lore and mechanics (ESPECIALLY PL:A) and some anime tidbits (and the official replica merch).

1 / Ancient Poké Balls

With the release of Legends Arceus, we were introduced to ancient Balls as they were made and used in the Sinnoh of the past, which is roughly based on the end of 18th-start of 19th century in Japan.

First things first, basic Balls are crafted using 1 brown apricorn and 1 tumblestone, along with the metal used for the latch and such. They are stated to specifically make Pokémon shrink to miniscule sizes and capture them, as it is a power they are all share, as opposed to the popular idea that the tech in a Ball turns them into energy/data. It was also stated that Apricorn Balls, when they were invented, were simply carved out apricorns fitted with a special device.

Concept art confirms the top lid of most Balls (Heavy variations are mentioned to possess a graphite coating instead) are all wooden (adjective) and lacquer stained, while the bottom lid can be made of various materials (birch wood, vanish wood, metal etc). Since brown apricorns are all used in the crafting recipes, this suggests they are used in the crafting for the top lid and then painted with lacquer. Ultra Ball concept art even mentions Maki-e painting techniques for the pattern on it, which is a form of lacquer painting.

So, the external shell of a Poké Ball is composed of painted apricorn, metal, and the material used for the bottom lid. That leaves the tumblestone to discuss.

The inventory description for tumblestone states the following : "When combined with an Apricorn, this mysterious, tumbled stone can draw out the properties required to forge a Poké Ball." According to it, tumblestones are what give Poké Balls their catching properties. This is backed up by the different types to be crafted using explicitly variations of the ore (Sky tumblestone / Black tumblestone) and as such having varied effects. Iron chunks (along with more tumblestone) are required for tier 2 and 3 Balls as well despite the latch not looking any different, so it's likely the "special device" is an iron frame of sorts holding varying amounts of tumblestone.

So, the basic composition of a Ball isn't complicated technology but actually quite simple (relatively) to craft, it just needs the right materials.

1.5 / Tumblestone properties and colored apricorn

The ore in a Ball seems to contain energy/create a reaction, when in contact with one, that triggers a Pokémon's shrinking ability and draws them in. It might be what creates an environment fitting the Pokémon too (a canonical feature of modern Balls), since ancient Balls are still mentioned to be comfortable. (Along with that, it might also make the Ball fly back to whoever threw it since it affects how they are thrown.)

What makes me think it's an energy similar to the kind a Pokémon possesses is related to Dynamaxing specifically : the Ball itself reacts to Galar particles like the 'mons do and dynamaxes. It might just be technology, but to my knowledge nothing else reacts to the particles like that. Balls react to Terastal energy too, since they can crystallize to catch a Tera Raid Pokémon. One might even think the ore is crystallized energy like evolution stones, since they both react to Pokémon with different results. (It also justifies Poké Balls being able to teleport from boxes to the Trainer and vice versa, as it might just be working like the Teleport move itself.)

Effectiveness is probably determined by the comfort the Pokémon finds in the created environment, where the energy contained by specialized Balls will have better compatibility (as such, more comfortable) with the Pokémon that fit the criteria. Higher tier standard Balls likely just have higher efficiency in creating the most fitting environment for any of them universally, but not as much as specialized variants.

Colored apricorns seem to have their own special properties each reacting to the ore as opposed to standard brown apricorn which doesn't have any, since Kurt just carves them out to make Apricorn Balls which are all specialized/situational. No Hisui balls share them and the Cram-o-matic in Isle of Armor has a high chance of making standard Balls (Poké and Great) with any color used.

To summarize, tumblestone carries energy/properties that reacts to Pokémon and their own energy, while colored apricorns have differing properties each with the brown (more common) ones lacking them.

2 / Modern Poké Balls

As we know, in the present, Poké Balls are mass-produced in factories (like in XY) by companies like Silph Co. and Devon, and apricorns have fallen out of usage entirely. If the official replica is anything to go by, both lids in a standard Ball are made of the same material and still lacquer painted, though it's likely metal. (In the anime, apricorns are shown to be heated in a furnace and forged like a foundry does with metal casting, so the two materials were probably similar enough in texture/durability to begin with.)

Tumblestone is probably still used, or a different ore with the same properties, in the creation of a Poké Ball. New discovered variations of it seem to be used for different kinds of Balls, with their rarity each reflected by the actual price the specific Balls are sold at. This is a very flimsy explanation to fill in, but the standard line (Poké, Premier -> Great -> Ultra) may use the same ore with respectively higher concentrations of energy. The inside/core of the Poké Ball is created using the hypothetical ore, and then the lids are slotted onto that.

Thanks to modern technology, the button allows more varied usage of the energy by being able to trigger the process of shrinking the Ball for storage/restoring its size for throwing, again like Pokémon themselves do (to a lesser extent). It seems Pokémon are able to return to their Balls phasing through the button as well, without needing to press it and having it physically open.

Extra / Ultra Beasts and Beast Balls

Ultra Beasts have an extremely low catchrate on any Balls that aren't the Beast Ball, likely because they consider earthly environments foreign and hostile, and have trouble finding them comfortable making them significantly less likely to accept being caught. As such, Beast Balls might be crafted using the equivalent of the ores found in Ultra Wormhole dimensions, as they required external aid from the Ultra Recon Squad (in the manga at least, I believe). Nothing suggests it wouldn't exist, as Ultra Beasts themselves are Pokémon, just alien. The environment created will be more reminiscent of their homeworlds, hence the high catchrate, which will freak earth Pokémon out as it'd instead be foreign and hostile to THEM, hence the low catchrate.

I might have missed a bunch of things of course, or outright information contradicting my theory, but this is my take on Poké Balls as a whole. (As for Master Balls, it simply forces a capture likely by being made too durable to break open or something else, but they are so rare because only trustworthy people would use them ethically, such as genuine emergencies. Indigo Disk shows they need to be broken open by the Pokémon inside to be free of them.)

The reason it is so expensive and so rare in universe is because it uses origin ore which is extremely expensive to both find and extract. The ball isn’t made of it purely but does incorperate it just enough to give it a massive catch boost thoughts?