Hey Waxworm, usually the deck of a boat like that is fiberglass over marine plywood. Over the years, that plywood can rot like any other piece of wood. In fact, fiberglass can rot if it is not covered with resin. That is why its important to slap some resin on any dings you might get in your hull. To answer your question, yes it can be fixed. If it were me, I would grind out a section of glass from around the drain and see whats going on under there. Perhaps you can take the drain out and see if you can feel around and perhaps get an idea of whats going on. I do all my own glass work but I am certainly no expert.
Fair Winds and Following Seas
Bill H. PTC USN Ret
Chesapeake, Va