I think the word deception is hard to use to describe the NSA Wiretap situation. To me, deception is an outright lie. The definition of deception on dictionary.com is a ruse or a trick. Based on that definition, deception is NEVER justified in the media. They have no right to lie, or "trick" their audiences. That is not their job, and they will lose respect.
If we used a different word, like omission, for the stories like the NSA, then I think that yes, there are times when the media should not report some information. Threats to national security is one of those. Many may not agree that the wiretap story was a threat to security, but it is possible that the NY Times understood more than the public did about the situation, enough to know when to hold the information back. I don't know about everyone else, but I personally would choose waiting a year for the story, than gettting the story when it was first received, and having something terrible result from it. That might be a little bit exaggerated, but better safe than sorry.