IMHO, the ship sprang a bunch of small leaks, and the reason the crew didn’t turn the crew compartment pump ‘on’ is that they were unconscious or dead already.
The jolt to the ship and crew from the explosion of their advanced design (IED) type warhead, due to their proximity to the explosion, was higher than planned.
If they were leaking, they would have had plenty of time to abandon ship. The sub sank quite a distance from its target. These guys were all still at their station.