Ive never had that problem i can usualy pull in 100k tons on 100% realism (i use a custom modified version of rub and other mods) with the viib each patrol, and still have most of my deck gun ammo left. Ive successfully wiped out a large convoy of all the ships of value (c2 or bigger) and still had several torps left. Of course with the IXB i could probably get close to 200k tons
Of course though i am a bit of a sniper with torpedoes, i can usualy kill most transport/tanker ships in one shot, and i almost never miss (and no i dont reload my save game if i do miss). I average about 1 missfire/dud/miss per patrol.
Ive also never used the 37mm for sinking ships as realisticly that pea shooter doesnt stand a chance on its own to sink anything but a tugboat. Oh and the mod i use its more around 1 second reload with fully trained crew.
I also generaly try not to duke it out with aircraft, risk vs reward isnt worth it. So i never realy cared much about improved flak towers
I should also add that in the custom mod i use, destroyers arnt total slouches in '39/'40 and often will harrass me for several hours. Though their dc's are usualy off.