How do you have your game set up? Mods? The major mods do change the damage statistics to make sinking more caused by flooding, and less due to destruction of deck-mounted parts. So feel free to shoot the deck gun, but it is better aimed below the water line, instead of stuff on deck. Also you need patience for the water to flow inside.
That said, if the sea bottom is shallow, it may be resting on it so it will never go below the waves. Though luck now.
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