Yes, what we know is that the NSA has compromised many vendors, including it seems some of the CA vendors. So it's possible that a CA could issue the NSA a certificate that could fool you into thinking an NSA surveillance node was a valid site, or that a bit of software was written by a legitimate vendor and is safe to run. The devil is in the details, of course...if the goal is to have a valid, signed Microsoft key, you really need the Microsoft CA to sign it, but 1) the vast majority of people don't check so close is often good enough, and 2) I personally think Microsoft would cave faster than Verisign, so...

And you are correct: if a CA has disclosed their root signing certificate, then the NSA could issue seeming legitimate certificates for pretty much anything.