Please make sure you read the User Manual. It explains in detail how ship sinkings occur in NYGM TW (or GW for that matter). The point is, you have to make the ship sink, not simply run out of hitpoints and explode. This means it takes a bit of practice to be effective in sinking ships as the tactics from the stock SH3 damage model will no longer work.
I can usually sink a medium merchant in 2 torpedoes and sometimes one (impact pistol). It is possible, but you have to be smart in your targeting.
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