In reference to question #1.
There is a mod called GWX all weather guns. It is JSGME ready, and once installed, you can use your deck gun and/or your flak guns in any type of weather.
There is also a mod that will temporarily stop the weather. The name of it eludes me at the moment, but you can do a search and find it failry easy I believe.
As far as hearing contacts on the surface. Its not too realistic. U-boats often submerged to 30-40 meters to conduct a sound check so that the operator wouldn't pick up any backround noise from the surface.