You're confusing "provable security" with "effective privacy", and they aren't the same thing.

Having uncontrolled supernodes certainly does "help you", as it means Skype can't see the traffic without some other exploit to get it. Verbal communication is normally "insecure" and subject to eavesdropping, but if I have the conversation on a boat in the ocean I can be relatively certain that no one else is going to hear it.