Another thread talking about the same issue, and my response: 255519287
I experience the same issue. It occurs when the audio stack crashes, and I suspect it happens due to mismatched sampling rates across various apps that can handle Coreaudio. It doesn't crash by itself, but I haven't been able to pinpoint a consistent way to reproduce. Sometimes closing an app does it, sometimes when the Mac is overloaded in resource use it happens, etc. But before my system audio / alert sounds stop working, I certainly hear or notice the audio stack crashing. One crash is all it takes to kill alert sounds, although Coreaudio does come back up. If you're not playing audio when the crash occurs, a crash is noticeable when you see your audio output volume resetting off its own accord.
Safe mode would not be helpful, but if someone knows how to find the relevant console logs, it might be a good start to debug this intelligently.