There's NES VC Console games people just inject roms into. So I'm thinking NES emulation on 3DS homebrew wise just isn't as big a priority, so the ones that did get made still have issues.
It is, VC injection is not perfect, especially NES one (lots of games don't work). GB is far better (only some rare few games don't work when injected).
Really hope to see an "FCEUMM3DS" update in the future to make it reach fullspeed