Pretty much. The code would have to be re-compiled in huge chunks or even fully which would be quite a feat for the feeble 3DS.The code would have to be extraordinarily good, perhaps even using some kind of huge static analysis of the entire N64 game's binaries before execution (which would constitute an on-the-fly "port", in a sense), for this to work within the limitations of the relatively slow 3DS. It will probably never happen, certainly not smoothly with any kind of real time emulation. Anyway, either code this or get someone to code this, speculating on it won't help anything ;-)
I also like how we're still ignoring the elephant in the room - Nintendo 64 games are rendered games at 256×224, 320×240 (can be scaled relatively easily to the 3DS screen, alternatively a border could be used) and 640×480 pixels. Assuming that the scaling will be performed on the GPU and the CPU won't be additionally taxed, we're running into the simple problem of being able to actually see stuff on-screen in some games here ...so enjoy the arse-looking scaling and terrible, unreadable fonts, guys! The 3DS's screen is 400x240!