The sound issues you describe sound (I'm not trying to be funny btw) like stock bugs that were never fixed. In rough weather (11m + wind speeds) large waves will wash over & submerge your watch crew. As far as I know, there is no fix for that. U-boat bunkers aren't water-proof either: rain will pour through the ceiling.
I would suggest that you download the GWX 2.1 mod available at
http:///thegreywolves.com/. It's a big download but well worth the time & effort. GWX fixes many of the stock game's issues & and adds a lot of new material.