My Mini 9 is almost dead silent. There is the smallest bit of electronic whine, if you put your ear right to it. I don't think I've ever heard a beep from it, but I've never challenged the limits of it's operation.
As for the speakers, search for motherboard pics on this site. They should show where and how they're connected.
Like any modern CPU, the Atom is designed to slowdown or even shutdown in the event of overheating. But I've never come close to the thresholds.
As for running with the lid shut, that's just be a setting in the OS's power management options.
I hope my answers were helpful.