Not sure of the stock game, but I don't think passing the thermal layer has any effect on sonar, it doesn't in any of the megamods.
Being on the surface the hydrophones work fine under most circumstances. The S boat doesn't work on the surface. A small depth issue may apply and most subs sonar works fine on the surface. In stock many of the subs almost ride on top the water, this can be a problem.
However, being at scope depth, I don't see that you would have a problem at any level. You should be able to hear ships yourself in the contact zone, 20NM's or so.
They're are a few ships when they run below 7kts, they don't show on sonar.
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