This may be the case for some emulators -- such as the NES emulator in excitebike. However, (if I understand everything I've read correctly) the SNES didn't have a 'sound chip' in the same sense that the NES (or GameBoy, C64, etc.) did. The NES and all of Nintendo's other hardware used to synthesize its sound in real-time, but that changed with the SNES, which introduced sample-based audio instead. (Fun fact: some people suggest that the N64's sampled audio can meet -- or exceed -- CD quality!)
These pages know more about SNES audio than I do:
http://chipmusic.org/forums/topic/217/so-super-nintendo/ http://en.wikipedia.org/wiki/Super_Nintendo_Entertainment_Sy...
I suspect issues with SNES emulation are simply that all of the SNES emulators we have are fairly poor in _all regards_, it's just that it's easier to notice in the sound than in things like timing.
Here are some examples of the other failings of many SNES emulators: