Managed to fix this on my own.
Checked out the submarine.cfg in my MODS folder and noticed that periscope depth was 14.5m for a type VIIB.
For a type VIIA it is 13.5m
So I just copied that line and put it into the type VIIB and VOILA, now I can see above the waterline with my Observation periscope.
Dunno what mod changed this or if it is a stock issue, but It was truly gamebreaking for me, not beeing able to use the observation periscope.
Though I canīt tell yet if the conning tower is sticking up above the waterline, cause I play with no external cam on. So beware for destroyers if you try this.