It's an interesting idea. I do notice audio stuttering when I play at 54 FPS, but if anything, that warns me that I need to check my settings in order to get back to a proper 60 FPS.

I don't know much about how audio works, but would a more user-friendly answer be to buffer 1 frame of audio, and then stretch the audio for 2 frames worth of time if the next frame isn't ready? This solution sounds much more complicated, but I would assume would provide a better casual gaming experience than having the audio constantly muting/unmuting during variable CPU load.

I wasn't thinking about casual play when I proposed this. You wouldn't expect frame times to vary much for casual play—as you elude to, a spike in frame times would probably be the result of misconfiguring EmuHawk or of another program hogging resources. I was mainly concerned about RAM Search hurting my ears while glitch hunting.