Yes, but the problem is that what is a "matter of national security" in practice is whatever the government says it is. So this exception is enough to effectively eviscerate the freedom of the press.
Press freedoms have not been eviscerated here. It's a trendy narrative, but in reality you have enormous freedom to distribute content which was illegally obtained as per the Pentagon Papers cases and others. The worst thing we have here is cozy relationships between the media and the government, but alternative news sources are available everywhere and Americans are relying on them more than ever.
Given the existence of NSL's (http://en.wikipedia.org/wiki/National_security_letter) there is no way of knowing who has been "asked" to keep quiet.
And when Glenn Greenwald visited the U.S. recently it was far from clear that he would not be taken into custody.
If they were asked to "keep quite" maybe we don't know about it huh?
They can keep you silent about the fact that you got an NSL (and that therefore there's an investigation going on), but not about the content itself.