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To answer your question, the only reason you would not be able to turn the bubbler off at night would be if that is your only source of filtration/water movement. Otherwise, you can shut it off.
So long as you have a filter that provides agitation, the air bubbler is really for show. You could put it on a timer so you don't have to remember to turn it on/off every day.
They're right. Your HOB should provide enough surface agitation without the bubbler. I recently put mine away, it was too noisy. But now my tank is nice and quiet.