Checking out the Civilopedia, I guess they have 2 first strikes, which isn't too bad. The lack of any ability to detect submarines or shoot down planes makes them rather useless compared to regular Destroyers, though. Especially since they have the exact same strength as regular Destroyers.
I guess you could get the best use out of Stealth Destroyers by combining them with a stack of other units... but then, what's the point of them being stealth units if they have to tag along with a rather obvious stack?

I guess we'll just have to write them off as a fairly pointless novelty unit for the late game.
Oh, another question while I think of it: How useful are Guided Missiles? I just realised that I've never actually used them in Civ4! I used to use them in Civ3 all the time, but I haven't seen reason to do so in Civ4 yet. Are they particularly useful in any situations? Seems to me that a few Bombers would be more useful than a stack of Cruise Missiles, but I might be wrong...