I did a test on the timer, saved mid patrol in a different TZ than Wilhelmshaven and reloaded. Both the ship clock and local time were showing what they showed when I saved so I'm not sure what the issue with local time is.
Other than that, I decided to compare the game world against this
http://www.weatherimages.org/latlonsun.html It's not very immersive, simwise (unless I could find one in German of course, like Kapitän Lazybutt ordering his nav officer to hand him the hours) but it would be interesting to see how well the game world compares to the real one at higher latitudes.
Luckily, SH3 doesn't mind me pressing the Win key in-game, so it's easily accessable.
One thing I wonder is, in real life, how did they keep track of the sunrise/-set hours when in the middle of the big, wet nowhere?