I'm in a similar position- returning to SHIII and running GWX 3.0
Taking on destroyers IS possible, but there appears to be a caveat:
My current patrol is feb 1945 and I have just retried a save position close to a convoy off the coast of East Anglia. I took out two of the escorts with homing torpedoes, hit another at point blank range, and just watched the 4th blow up through my periscope, having hit it with a stern torpedo from 350m, at which point the game froze and seconds later crashed to the desktop. This is the second time the exact same thing has happened!
A George Russell moment if ever there was one