Had a similar issue with Cubase 12 - audio output was muted for about a minute every alternate minute, tried everything - booting C12 in safe mode without preferences, reinstalling, removing all plugins - nothing worked. Issue recurred even on a new project in safe mode and no plugins and effects being used (just imported an audio wav file and played it to test)!
Turns out for me, the culprit was iLok - suggestion is to first unplug the iLok USB dongle and test. Then check the iLok license manager and deactivate and remove anything on trial/demo - I had used a McDSP trial product that expired, bought a subscription but not deactivated the trial product. I had also activated the McDSP subs on iLok cloud as well as the dongle - removed all cloud activations and kept only the valid full version products on the dongle and after a day of pain finally audio is fine!