Were these problems ever fixed?
 

Back when I first played SH4 I remember two annoying bugs and I wondered if any of them ever got fixed?

1) Crew not having any eyes

2) Specifically in the UBoat Missions Expansion I remember a pretty bad bug that was confirmed regarding the UBoat not responding to the waves as it moved through the sea.

Crew not having eyes - I have heard alt-tabbing out of the game is what causes this, and is to be avoided at all costs. I have also heard that turning off 'volumetric fog' in graphics options can help resolve a lot of graphical glitches with the game. I am fairly alt-tab happy. I just ignore the missing eyes if it happens, which is rarely. It doesn't really affect gameplay.

Uboat not moving in waves -- I have never seen this one happen, sorry. I do know a lot of gameplay bugs are caused from corrupt savegames when you save with lots of other ships in the area. Avoid saving while near a convoy or enemy ships and try to do your saves in the open ocean, or in port. I used to be obsessive about 'staying alive' and saving constantly, but I just learned to not care and load up the next campaign when I die instead .. It's more realistic anyways that way ;)

All that being said, any bugs that were present in UBM when you played it are still there. UBI never issued a bugfix patch for the game, and never will.