Sound On enables playback of sound (it's essentially always still emulated though). The "Toggle Sound" hotkey can control it.
Mute Frame Advance will disable small 1-frame sized sound blips when using Frame Advance (see Speed & Throttling). This is enabled by default, and I'm not sure why it's even an option. Does anyone know why you might want to disable it?
You can select from one of several Output Methods. Fiddling with those and the Buffer Size may decrease your latency.
BizHawk is also doing some complicated things like retroarch's "dynamic rate control" to kind of smooth out audio, but it doesn't do as good a job. There's no way to disable it and you may hear it from time to time as a kind of warm old-VHS tape pitch warbling. It's especially noticeable on the PSX core where there is some kind of weird interaction with mednafen's sound code. Listen for it when the bios screen boots up. In the future it would be nice to make this all more tweakable.