There's no way the 3DS can handle N64 games. The system's just not close to powerful enough to emulate the N64 CPU. (Make no mistake--VC games use software emulation of the original hardware running the original code, which is why no SuperFX games like Star Fox are available: it's a separate in-cart CPU and no one wants to worry about the sync issues).
So while an N64 could be ported to the 3DS with vastly superior graphics, actual emulation of the original is out of reach.
I'm surprised they don't have classic DS titles on the 3DS Virtual Console, to be honest. I can only imagine it's a memory mapping issue. (They could offer them as "Virtual Consoles" or not, but I think eShop access would be a boon.)