The emulator is a port of the FCEU emulator (Not FCEUX, its an older version of it), and the only inaccuracy over the original NES is that it runs at ~59.85 FPS. I know that it wont be allowed for Any% WW runs, but I just wanted to know if I could use it to run other categories since I already got an 11:15 on noWW playing on this emulator and its my only way to play it now.

Never heard of that one, points for obscurity.

The other 3 categories say "Banned emulators: ZSNES (any version), SNES9x 1.4x". Since FCEU is not explicitly mentioned, and the smb3 folks are pretty chill anyways, you should be safe.

If you do anything to obviously expose some difference , the run would probably not be accepted and the emulator likely banned. I am quite sure the reviewer would notice :)

Good luck, hands have mercy!