My estimate would put it at around 4-5 "real" decks. There'd be the "engine deck," one or two "mech/fighter/cargo decks," the "quarters deck," and the "command deck." The "engine deck" would probably have a few sub-decks and the "mech and fighter decks" may also have multiple sub-decks while being mostly cubicles.
I could reasonably see as many as 12 decks based on the size of the ship, but I can't see what would reasonably be contained in them, so stuck with a much lower number.