@Citro Figured out the issue. Had nothing to do with the emulator; for some reason, the affected roms were 0Kb in size... not sure what happened, but when I re-copied roms to the Pi, they worked perfectly.

Thanks again @columboscoat

I tried them both now, and nestopia definitely has the better audio emulation. Mario 1 dying sounds so inaccurate in fceumm. In the past, nestopia had this strange sound bug every now and then but I no longer hear it. Though, maybe the fceumm audio accuracy might be improved in the future?

And can I recommend having the Unsaturated or Nes-Classic Palette as default? They look much better on both emulators.