Gonna have to be more specific as to where the deck is making the popping sounds. Best thing... take a picture and mark on the picture where it makes the sounds. It could be two pieces of fiberglass flexing against each other (hatch/deck) or it could be delaminated glass. "Fixes" will range from tightening screws/applying caulk to a $10,000 deck/stinger/bulkhead repair job, or more.
