How's the weather? If your boat is dipping beneath the waves regularly you should get hydrophone updates then. The main hydrophone array is built into the sides of the boat near the bow. It is possible to have the improved KDH sensor, but that is actually mounted on the deck, so it would definitely only work while submerged.
I've never experienced that particular problem, but it sounds like the 'silent running' bug: if you surface while Silent Running is set, your crew will still not do anything until you secure from it. Likewise you cannot open torpedo doors below 25 meters depth, which is okay, but if you go that deep with them open you then can't close them either!
