After 1942 the deck gun is almost useless . Even small merchants have at least 1 decent size deck gun to fire back at you. As for the small ships I usually fire only 1 torpedo. 90% of the time a Magnetic shot will sink them with no problem. Sometimes it takes 2 but not often.
As some of the other mates here said tonage is tonage, get what you can get.
As for that air cover...... the later it gets in the war, the thicker they become. GET THAT SNORKEL.