I have sunk previously torpedoed - and thus damaged - vessels with my flak guns firing armor-piercing shells when I'm out of eels and deck gun ammo but REALLY want that last ship to go down before returning to port. I even sank undamaged fishing and tug boats with 20mm.
However, the amount of time spent on the surface doing so is dangerous as you may suddenly have unwanted contact with aircraft or a destroyer answering the call for help.
However, I don't see any real difference in the amount of apparent damage inflicted by the 37mm vs. 20mm flak.
My deck gun has a lot more punch.
I rarely use my flak guns on a patrol