Did you save the game before you expended all of your deck ammo? If not, start a tutorial mission and put at least one fish into a freighter and then manually fire the deck gun at one spot in the water line. It's a lot more effective than just riddling it full of holes in random locations. Above the water line the ship will burn, you may destroy some deck guns, and/or an ammo crate might explode, but that's about it. A tanker full of fuel may be a different story... assuming that the devs modeled empty and full tankers.
Basically, NSM calculates sink rate based on the amount of damage to a compartment below the water line and the number of compartments in a ship that are damaged and healthy. It also depends on the skill of the damage control team for that ship and how well armored the ship is - or at least it's supposed to be that way.
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