I guess you don't dive deep enough. For your sonar/hydrophone operator the boat must be constantly below 9 m depth. If you have bad weather and only went to periscope depth, you probably hear nothing (and that's quite historically accurate). If that's the case, go deeper, to 20 metres, some prefer even 30 metres.
Sonar is not supposed to be working when on the surface.
It may also be a game bug - sometimes your boat and crew just ignore being submerged and behave like the boat was surfaced. This could also be the case. [Sometimes reverse happens - on the surface boat still thinks it's submerged]