As much as I like the gun for damaged ships I rarely use it against the later armed merchants, especially liberties and such. But still I don't see a reason to remove it altogether as you can never know what good it could be some time.
I also don't believe that it's modeled in SH3 as I read somewhere that the deck gun increases underwater noise produced by the sub. Concerning all the flaws and bugs of the stock game I just cannot believe this detail would have been implemented.
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