AFAIK the 1/1 model in Das Boot wasn't a working replica, but a "waterline model" at least in the harbour built onto a couple of empty barrels. This model ship was towed with the crew aboard.

For the other shots several models were used, those can be seen in the museum of the Bavaria Filmstudios. Including the conning tower and the interior model which was told to be an 1/1 replica of U-995, except that it has darker colors.

When we've been there with my wife (as part of our Honeymoon trip), there was a short movie too which explained how some parts (burning ships, explosions) of the movie was made in a pool.