New here... If the 3ds/2ds is stronger than the N64 (I think it is) I would love to see an N64 emulator. I am a noob to this coding stuff, so I would not know. Considering that N64 games have been ported and updated by Nintendo, I think its possible. But maybe the older Nintendo hardware wont work on the 3ds? IDK.
In order to run an emulator properly, the console itself has to be 4 times more powerful than the console you want to emulate, not only that, the console has to have the amount of buttons necessary for you to port, let's say, you want to emulate an Nes which has 8 buttons in the controller, but the more powerful console you have only has 6, and so, the N64 is more or less like that, even if you could program an emulator for the 3DS by using the Circle Pad Pro, considering the amount of arrow buttons in each part of the N64 controller, you still have to manage the coding and processing resources, the main architecture of the N64 is quite complicated, even today PC N64 emulators has some problems emulating some games for the console, there is some graphic glitches, down run on FPS, etc. Even the Wii (Which is slightly a more powerful console) have problems with N64 emulation, though, there's going to be a new version of Wii64, so, that's something good.
So, no, the actual scene doesn't have the resources to make something like a N64 emulator when they're still experimenting with the SNES emulator, which is far more easier to emulate, so, if you still want a N64 emulator for the 3DS, you'll have to wait, a lot, especially because even if you found an actual working n64 emulator for the 3DS, chances are that is still beta, and it will need some years to fix it, so, in order to do that, you'll have to wait 2 or 3 years at best in order to perfect the emulator for the 3DS, but by the time that comes, the 3DS will be outdated by another portable Nintendo console, and everyone will put better efforts in hacking in that new console respectively, at least you can play gba games on your 3ds though.