I’ve had this same issue previously while running Ubuntu on my previous media computer.
During any and all playback, there are audio issues, taking the shape of minor, yet frequent crackles and pops.
I used to run Kodi on Windows, and there were no sound issues there.
In short:
RPi3
OSMC (2016.12.01)
Sound and video over HDMI.
Audio crackles and pops.
Tested:
Fiddling with the available audio settings and outputs.
Installed PulseAudio, tried it as output and applied the tsched=0 fix.