The aircraft could have been deliberately sunk for training. Or, it
might have hit debris in the water or a submerged object and received a
whole punched through the fuselage. Lastly, water pumps might have
failed causing it to sink gradually between pilot visits.

Of course, Captain Zoom is known to operate a U-Boat in the vicinity of
the EAA seaplane harbor in Wisconsin. Not that he torpedoed it or
anything. It probably smacked him in the periscope upon landing.

You know, the thing he looks down his nose at to watch USENET from in
the submarine's Conman tower...