I rechecked this morning, but in Blair's U-boat book, vol.1, Prien stated that he was on the surface when he went into Scapa Flow, no mention of "decks awash".
You can find many photos of subs with flooded decks when they were in a static state in calm water, i.e.:
http://www.history.navy.mil/photos/s...sh-s/ss105.htm
USS Chivo moored with decks awash:
http://www.navsource.org/archives/08/08341.htm.