It ain't easy. I've attacked Scapa Flow in 40' and they strung nets up and mined the western approach. I've also attacked Gibraltar though and I found that to be easier (deeper harbor depth). If you do decide to attack scapa flow, remain at silent running at all times and do it when the weather is at the worst that it can possibly be (1km visibility)
http://www.subsim.com/radioroom/showthread.php?t=167025