I may be misinformed, but when those Estonian programmers wrote Skype it was at the time both decentrialised and encrypted by default. Is that not the case anymore? A pre-emtive apology if I remember the story incorrectly.
That is indeed not the case anymore, as per the PRISM program, which was leaked during the Snowden leaks of 2013.
From Wikipedia [1] the following three quotes:
"The documents identified several technology companies as participants in the PRISM program, including Microsoft in 2007, Yahoo! in 2008, Google in 2009, Facebook in 2009, Paltalk in 2009, YouTube in 2010, AOL in 2011, Skype in 2011 and Apple in 2012"
"Internal NSA presentation slides included in the various media disclosures show that the NSA could unilaterally access data and perform "extensive, in-depth surveillance on live communications and stored information" with examples including email, video and voice chat, videos, photos, voice-over-IP chats (such as Skype), file transfers, and social networking details."
"According to The Guardian, NSA had access to chats and emails on Hotmail.com and Skype because Microsoft had "developed a surveillance capability to deal" with the interception of chats, and "for Prism collection against Microsoft email services will be unaffected because Prism collects this data prior to encryption.""
Regarding that last quote, Wikipedia mentions these sources [2] [3] [4]
[1] https://en.wikipedia.org/wiki/PRISM_%28surveillance_program%...
[2] https://www.theguardian.com/world/2013/jul/11/microsoft-nsa-...