I have also noticed small clicks/pops in HDMI audio in Kodi, not on LibreELEC but using a custom build of Debian Buster with 5.3 kernel.
If the CPUfreq scaling governor is set to "performance" it doesn't happen for me.
If the governor is the default "ondemand" I hear the clicks. So I suspect it's related to CPUfreq switching frequencies.
and then test HDMI audio. It'd be interesting to see if that fixes the issue.