I think the allied subs are actually ships with a submarine skin. They are made with a gazillion hit points and tough as nails = indestructible = Don't waste your time.
The enemy 20mm (aircraft included) problem is that they seemed to have titanium tips which are able to go right through your sub, never mind the earth. I made a little mod (from NYGM -but you can do the same with GWX)
http://www.subsim.com/radioroom/down...o=file&id=3845 that reduces the penetration power of the 20mm APs, so that only rockets, bombs, and something bigger than 20mm can do hull damage - Carefull as you can still lose crewmembers.
Edt: I modded the aircraft 20mm here, but have not checked the whether ship 20mm use the same gun data. This might be different which will mean you still will look like a sieve. Tell me if this still happens and I'll do a fiddle.