Some systems use both above and below water hull. If everything above water is destroyed the ship is practically useless (guns and superstructure are holed, burned, or otherwise missing from the vessel) where as if all below water is gone, she will sink.
In shallow waters a ship with all the below water hull will settle on the bottom, but if the above water hull is still useable, the effort could be made to rebuild or reconstruct a vessel (50%....all the bottom, 75%.....all the bottom plus work to the upper works).
Some rules have it that ships get lower into the water as they loose floatation, so the vessel might not be completely "sunk" just that she couldn't float wtih high eoungh without touching the bottom of the harbor. (she ran aground sitting still).