While it would be possible to implement Nintendo 64 emulation on the Nintendo 3DS. Unfortunately it would be limited in the capability of what it can do, if it was made as an app.
The best solution would be to develop an NUS_FIRM partition from assembly language, or some application that installs an NUS_FIRM partition onto the Nintendo 3DS system. Only that would provide optimal play and reach the limits of what the ARM11 and ARM9 processing cores can do. Since what we're handling here, is converting all the MIPS instructions into ARM9 and ARM11 instructions, which has to be implemented in the same way as AGB_FIRM is written to convert ARM7 instructions into ARM9 instructions.
But the thing is, the NUS_FIRM will have to be bigger, because all the instructions have to be converted, where as the AGB_FIRM only has to convert certain instructions of ARM7 into ARM9 (since most of their instructions are identical to each other).
I'm positive that NUS_FIRM could also be implemented on the original 3DS, but we should aim for New 3DS first, seeing as it has a higher clock-rate and more RAM.