I found a good workaround. If I disable auto suspend from pulseaudio, it seems that I can prevent the whole audio stack to go into suspend mode, thus avoiding the loud noises upon suspend and resume that I hear through my SPDIF to DAC to Speakers.
The workaround is to comment this line in /usr/local/etc/pulse/default.pa
### Automatically suspend sinks/sources that become idle for too long
load-module module-suspend-on-idle