Governmental -- i.e., public -- communications are supposed to be available for review. Certainly, the Secretary of State can legitimately claim national security issues, but using an external system just gives the appearance that Clinton would like to be able to obfuscate even-legitimate internal requests for her communication. For instance, the paper trail about Bengazi is already damning enough. I'm quite sure she'd like to avoid showing her office's internal -- and her personal -- correspondence on this issue. Unless you're suggesting that the NSA would present that communication (which I agree they have access to) in court, I think this is a non-sequitor.

The problem is not that the government doesn't know about them, it's that the PEOPLE don't know about them.

The NSA doesn't seem to share much with other agencies. So most of "the government" might not know about it.

Define "The Government", it's not a single uniform body, various branches and factions work with and against each other.

It's not the NSA we're worried about. It's that Secretary Of State Hillary Clinton was receiving, storing, and transmitting official secrets illegally on a secret personal email server, subject to extreme risk of antagonistic foreign powers snooping that server and acquiring those secrets. One may wonder why she would arrange such a system in her own home. One may wonder if she wanted such covert foreign access to such documents, the security risks being so obvious.