I've done a little research, and it looks like I was wrong. I was under the impression that, even though consoles like NES and SNES have resolutions in the 200s, they still output a 640x480 signal. But it looks like that is not the case.
So, NES, SNES, and N64 could all fit on the 3DS lower screen, which is 320x240 - the exact same as most N64 games.
Now, this doesn't take into account that VC games are designed for the Wii emulators. The 3DS would use different emulators and therefore the whole catalogue would have to be reprogrammed for use on 3DS. And that isn't worth it, unless they charge for them.