My understanding is that after MSFT acquisition, they don't use their customer devices as supernodes anymore [1]. For "silent hole punching" with UPnP, that is very much business as usual for any VoIP application as well as other applications, such as Windows' Teredo IPv6 thingy.

[1]: Ars Technica seems to confirm: http://arstechnica.com/business/2012/05/skype-replaces-p2p-s...