WELCOME ABOARD!
I know that ships have a limited number of depth charges in SH3, so they should in SH5 as well. How many ships are attacking you? If one carries 36 charges then two or three might easily bomb you one at a time for a couple of hours. What year is it? Later in the war destroyers can carry over 100 charges.
As for the flooding, a depth charge can shake the boat, breaking pipes and valves, but still not damage the pressure hull.