I think they can bark for different reasons. The main one that I know of is a warning call to the rest of the colony. Sometimes when something moves across the room they will tell the others "don't move! danger!" I'm not sure how many you have, but if you watch closely, usually when one starts barking, it and all the gliders around it will freeze in place. Then if you move towards them, some might scurry quickly back to their pouch to hide. In the wild, I imagine if one saw a big shadow moving by (could be a hawk!) they would bark and the rest would freeze to not attract the predators attention. Then if something did actually move towards them, they'd hightail it back to their nest ASAP!
I've also heard that they may bark to seek out other gliders or get their human's attention because they are bored or lonely. I'd had one that was barking all night and I went in to check multiple times and tell her to shush, pet her, give her a treat, etc. Every time I went in she would stop but as soon as I left she'd start up again! Her barking was stressing the others, so they all went back to the pouch and stayed there, not a good strategy if you are lonely. I finally took her out and let her run around my room (an unfamiliar place) and that kept her entertained and quiet. It was her way of telling me she was bored and wanted out of the cage.
It's a common thing for them to do, but they don't necessarily do it every night. It is much less common if they have a buddy I think. As for what to do, I think it is generally better to ignore them as rushing in to them every time or giving them a treat every time reinforces the behavior (when I bark, mommy comes!) If it is a lone glider or barking for an excessive length of time I would take it out to play. If it seems very loud and frequent, I would definitely check to make sure they are all ok!