Im pretty sure arming the crews of the ships (even u-boats) was just as a precaution and was not really intended for any kind of offensive use.
I could see them being used in capture scenarios - like if the boat crew wanted to(and would expected to be) try and fight off someone capturing their boat or in a more extremely rare case, some kind of mutiny.
I don't know about the US but our (Canada) ships still carry small arms on board. "Just in case".
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