Regardless of the games take on this. A Uboats 'skin' and hull was very susceptible to small & large caliber fire. So as soon as merchants etc became equipped with their own deck weaponry, surface attacks became dangerous.
So uboats opted to remove the now useless (or less used) deck gun in favour of faster turn rates, reduced drag , faster dive times and (possibly) additional storage resultant from the removal of DG ammo stores.
Why have it if you can't use it?
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