Here is my, in my humble opinion slightly better answer:
Because encryption and decryption. Most modern game systems protect the game executable files, assets and metadata with encryption. The console holds keys, usually a common one, a console specific one and purchase specific one to decrypt files as they are accessed and there is specific system firmware/hardware/CPU code/hardware/instructions/etc. for the console to make this a seamless process. Vita3K
can do this decryption if I recall right, but it can be slow, if not even impossible on Android as far as I understand. The process might take a long time, or be unstable. Playing a NoNpDRM as is on Vita3K might suffer from slow load times or slowdowns as for the emulator, or not work at all, especially on Android as I understand. This on the fly decryption might take more computational power than it does for a real vita.
Vita3K versions are the same game files but are decrypted usually using a real Vita. A tool named "French American Game Decrypter", or, "FAGdec"

, is used on real vita to make copies of main executable files in decrypted, and easier to access format, and rest of the game is also copied over decrypted so the whole folder can be just ran without that pesky decryption.
Lastly the size difference: Main culprit there is the part that says "English Patched" and difference in how this is achieved on real vita hardware versus emulation. Or, how similarly: On Vita, because of the encryption, you cannot just replace the original files in their system location. You need a plugin named "RePatch" that forces games to accept additional content sources that can have modified assets and even executable files in decrypted format that will on-the-fly replace the original files. You just cannot replace the original files on real vita because again, they are encrypted and there is an expectation of encryption or things will go south. This is very similar to how 3DS, Switch, etc. also have their hacks and translations achieved.
On Vita3K, a good fellow will just replace the original files with translation ones; you can just do that since both are encrypted and that all is cool, and saves space by eliminating duplicate files you are not actually even using. On real vita, you
can delete all the original asset files in Vita's system level /app/APPID##/ directory that RePatch content replaces and the game will still work, and minimizes space taken by duplicate files, and ends up usually exact same size as "Vita3K" version this way. This is what I done on my own Vita and also uploads I have given out. One interesting possibility enabled by this setup is using translations with real game cards on vita. But people usually use microSD adapters that go to the game card slot on vita systems so you would need to not do that, and use pricy, small and expensive, if not also rare vita memory cards to store all your translation files etc. Decrypted and Encrypted files do also compress bit differently but it is not the whole story in these cases. If you see
Metal Max Xeno upload on Repo, english patched both versions take the same space. I handled this upload originally in requests and made the NoNpDRM version for real console in manner I described; deleting files that were unnecessary for a translated, size minimized and playable NoNpDRM upload.
3DS is same for example. This is why it is not actually possible to copy paste pirated roms to 3DS SD card and just run it as there needs to be system specific stuff, the files have to be in base encrypted form to be accepted and all that jazz, and on it goes with PS3 and PS4 and Wii U and so on. Even PSP (digital only?) IIRC. Even DS though for these the encryption was simple enough to be universally, simply defeated by digging out one hardware key. Vita is obviously not that simple. Also PS3 might been encrypting only executables not content, maybe.
TL;DR: Modern encryption standard in console game delivery and storage that changes how things need to be done with emulation file access and making it computationally and storage wise easier for users of Vita3K by offering them a ready made "conversion". Also translation patches are essentially duplicating files on NoNpDRM format unless "optimized" manually.