N3ds physically has more cores. It will just crash, along with all n3ds exclusive games.
@TheGreek Boy just use the standalone snes9x emulator, it should run it at full speed:
https://gbatemp.net/threads/snes9x-for-old-3ds.435568/
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To add onto this, the snes vc emulator on n3ds has near perfect accuracy to an original snes, which requires more hardware to run and synch perfectly. Since snes9x ditches accuracy for speed, games run much faster, though there will be some things that don't perfectly line up with an original super Nintendo. Mainly that if you hooked up the same inputs to the snes vc and an original snes, both games would be in exactly the same place no matter what you do. Snes9x on the other hand might be out of synch, such as Mario missing a goomba or a jump. Not noticeable to the average player, but a big deal for nintendo.