Is it any different than having a Luftwaffe fighter or bomber in a museum in England(or any other country for that matter)? They caused quite a bit of death and destruction as well.
I don't think a museum piece or display "glorifies" the Nazi regime. It is part of history and needs to be looked at as such.
I doubt the U-Boat display has any type of glorification type plaque to the heroism and memory U-Boat crews or Naziism. It is just an artifact that the curious can look at and see a weapon used in the past.
Now, I'm a 44 year old American with a love of history and the study of WWII, so Europeans may have a different take on this since the war was so much closer to home. I'd be interested in hearing other opinions on this.
I've always found it interesting how U-Boats have been so villified while the American submarine offensive against Japan can be glorified at times. America was trying to do the same thing as well and not all American and British submariners came out of the war smelling like roses. I guess a lot depends on if you're on the winning side or not.
Just my $.02.