The location of the "supernodes" (on client machines, or in a datacenter) is separate from whether encrypted traffic can be read by a third party. Using a totally decentralized system makes it a little harder to eavesdrop, but it's entirely possible to develop a completely secure system in the centralized model.
That said, I've never been terribly impressed with Skype's security model. Even before Microsoft bought them. It might have been decentralized, and the traffic might be encrypted, but the encryption lacks a strong trust model. There's never been any way to make sure that your connection hasn't been MITM'ed, since the system doesn't provide any way to verify the identity (key fingerprint) of the person you're talking to.
The current encryption is fine if you're worried about rogue network administrators, but has never been sufficient if you're worried about being targeted by state actors.