I can't remember which interview it was, if on Democracy Now, or his MIT lecture video, but Bill Binney stated that the NSA in fact does decrypt HTTPS.
They still don't have the private keys of the sites if they break into the CA.
Also, given that the world's best engineers work at either high-tech companies or the NSA there will be some who have switched between these industries, giving the NSA/CIA a headstart to get any information these companies hold through old-fashioned spy-tactics.