There has been much debate about the general repair and appearance of the U-boats & the best that we can come up with is........
When they returned to port, they were stripped & repainted to look as new.
Conversely, when the IX boats returned from thier long patrols, they were indeed 'weathered' but unlikely to be rusty.
Now, there is no allowance within SH3 to have your skin change mid-patrol so, each to their own.
You can find, arguably the best skins in this thread -
http://www.subsim.com/radioroom/showthread.php?t=88849
If you can be bothered, you can find mine for the IX series.