My guess is you have a large galvanized tank and either it doesn't have an air volume control or the AVC is toast. I'm guessing that you also have some method of introducing air to the tank, like a bleeder/snifter/checkvalve. It could also be that you have an iron filter with a micronizer or air pump.
As for why there is air moving through your pipes at night, there must be some sort of water consumption at the time. Either a softener or iron filter backwashing, or irrigation on timers.