I can agree about not using flak guns on ships normally but in this instance I am using the S-Boot mod. I have only 2 tubes and a total of 4 torpedos. I do have 2 20mm cannon and a 3.7 twin barrel cannon.
If the ship doesn't sink with 1 torpedo, I use the 3.7 with armour piercing rounds which usually gets the job done, eventually. Luckily I carry lots of ammo.
Sadly, the crew won't fire these guns at ships only aircraft (of course) which means any shooting has to be done by me. Try running away from 3 destroyers, dodging and weaving, firing the guns, micro-managing the repairs service and keeping all your fingers crossed as well as rubbing the lucky rabbit's foot!