I'm sure they can "ask nicely" to get a working cert from a CA. It's why newer versions of browsers are implementing certificate pinning, which should help (but not solve) with the issue by locking the browser to a specific certificate.

I would continue under the assumption that they can and do. If confidentiality and authenticity is mission critical, you need to be using a hidden service rather than relying on SSL. A hidden service does not exit the network and does not rely on external validation.

If you're running secure site, you should use your certificate & signature. Even then NSA could well be capable of creating fake certificate, but it would be expensive. But that would stop others without huge computing capacity. Of course this requires that you're able to deliver your own CA information securely to your site users. Also end users should disable trust for any browser/OS build-in CAs.

To answer a complex question: SSL/TLS isn't the problem, the certificates are.

Do they really need to fake it? It surely might be a part of the famous indirectly accessed data.