This is true in some cases - I guess they would say they're not relying on obscurity, but all the same they're going to use it. But of course, this is sort of foolish, since a crypto system whose security is improved by obscurity is one that's so completely broken that you wouldn't use it in any case. The only way this might conceivably help you is if you're using some system and a new attack is developed for that system - this would buy you a little bit of time to change systems, I suppose.
And of course, trying to keep your protocols secret only helps you when you're in control of both sides of the encryption. So basically, it's going to be possible for storage and for your corporate intranet and stuff like that.