Given the guts of the Home Fleet had largely relocated to other ports after the sinking of Royal Oak in 1940 and that the defenses of Scapa had been upgraded by a fair bit since (IIRC U-47 got through a channel that the poms were going to place blockships in -thus forcing any subs trying to infiltrate to run on the surface and so ge tshot to pieces- but the poms hadn't had the chance to yet).
They didnt just sink blockships they actually built causeways to link some of the smaller islands. So unless the U-boat had wheels it wasnt getting in. Prien in U-47 had excellent timing a few weeks later and his route in would have been blocked. I know everyone thinks the Royal Navy was run by morons soaked in gin but they only tended to make the same mistake once.
Some great photos of the Orkney barriers and defences.http://www.orkneypics.com/webpage/page/page011.html