I asked this same question about SH3 a long time ago. I think the general consensus then was that sub captains used whatever tools they had available to survive.
I 'm sure that there is a limit as to how deep you could raise the periscope without damaging it, and that there are times when the water is just too murky to see more than a couple of feet, but if conditions are right and you are above that critcal depth, why wouldn't you use it?
I believe there are times when the periscope could be used easily and effectivly underwater and I doubt that real life sub captains would disregard a very usefull survival tool because it made things too easy.
(EDIT: The fact that you can raise the scope at periscope depth indicates it is watertight, and if I understand correctly, the periscopes are allready filled with fluid are they not?)
My two cents.
