Thanks for the info, but I have more questions.
1. Can someone look into folders present on 3DS's SD card by using an SD card reader? Currently, I don't have one.
2. On my PC, I have NES and GBA ROMs, which are files with .nes and .gba extensions. How this is saved on 3DS? The same way or different, more complex?
If the same way (.nes and .gba files), then I could just put US Minish Cap on EU Minish Cap's place, keeping the exact same file name. Heck, I could even put completely different ROMs (like replacing Metroid with Mother 1 and one of the other GBA ROMs with Metroid: Zero Mission, because it includes original Metroid as an unlockable bonus).
If more complex way (like Wii's .wad files), then replacing ROMs will be difficult. In this case, I surrender.