A u-boat had two kinds of hydrophones. One is in a array in the bow. It can't hear straight forward or aft. It also can't hear on the surface because the bow wake is foaming all around it. The second type is mounted up on the deck. I works better than the first type but can't hear while surfaced because it's not even in the water.
A surface ship has the hydrophone and sonar projector in a dome underneath the ship. It is specifically designed to hear submarines underwater, or else it wouldn't work at all. Funny thing is, it can't hear you while you are surfaced.
The hydrophone hearing underwater in SH5 is a holdover from SH4. SH4 let submarines hear while surfaced because the American subs had their hydrophones and sonar gear in a dome under the keel of the sub.