[1] http://en.wikipedia.org/wiki/Skype_security#Flaws_and_potent...
For all we know, the core Skype protocol may be perfectly implemented. The Wikipedia link states there's no peer-review.
As a corollary, just because you can't do a quick Google search for 0days in iOS or Windows doesn't mean they exist. In fact they do, and they're bought and sold on black markets or are kept secret by governments and the like.
You don't assume something is secure because you can't readily access documented flaws. You assume something is secure when it has undergone rigorous peer review, which, as you stated, does not exist.
Your argument seems to be that you can't simply find a laundry list of Skype flaws floating around. This is true. But it says positively nothing about the security or lack of security regarding Skype's protocol.
I agree that Skype's protocol may be terrible. But you cannot state that obscurity didn't help. "No one" is even able to connect to Skype, let alone break it, at this point.