This is not a mistake, it's a feature: download retail games instead of buying a cartridge.
Advantage: you can have multiple games on the SD card at the same time, no need to transport all your cartridges with you.
it's now a common thing to buy and download games (steam, 3DS, WiiU, etc.)
Decrypt require a common key (stored and used by the console. can be found if console is hacked)
Encrypt require a private key (stored by Nintendo HQ. Nobody can find it)
the 3DS requires that the game is encrypted, so if you decrypt it you can't re-encrypt it to play on another console.
Decrypting will serves no purpose except looking inside and extract content (pictures, sound, etc.)
If you have more questions regarding what's possible or not to hack the console or bypass security, I think it will be better in the stickied 3DS hacking theories thread.