The answers to your questions can depend on the date in which your patrol is done. Remember the GWX patrols can start before the war broke out. Some countries and ports may still be neutral depending on the date after September 1939.
In the first patrol tonnage and renown may not be awarded if you changed upgrades or crew on your boat. It is best to delay those changes until you set out on your second patrol.
As for hydrophone operation above water, this may be related to heavy wave action. The hydrophone should not be working until you are below 10 meters depth. You may be diving into a large wave when it temporarily becomes operational.
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