There's a slight delay as the crew mans the guns.
It's best to simply look at a target you want to fire at and press spacebar to mark it as a target. It'll man the guns and fire on their own. Surface the boat to stop firing. (this will all be fixed with the next patch, should it ever come out...)
Or use something like TDW's NewUI for SH5 which includes full controls for the deck gun from the officer command bar.
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