It may just be a gag order thing, sure. But with the level of access required for stuff like this, I don't think they could shut the whole team up. How many people worked on this Microsoft back door? It can't have been less than a couple dozen at least. And none of them raised the issue or let someone know, a journalist for instance, or publicly raised the question?
It makes me wonder about the true extent of the programs we're freaking out about. I mean, of course they exist and they're big and threatening, but I don't buy that they could combine complete access with complete secrecy. They need the cooperation of the companies, and the companies, by NSA standards, just aren't trustworthy enough. In fact, they're full of wild cards like Snowden, denizens of newsgroups, IRC, 4chan, etc, who would LOVE to be the one to blow up an NSA attempt to write a back door into Skype.
Maybe they did, and it all faded away. But it just seems strange to me that so little has been said about the elephant that must surely have been in everyone's room for the last few years.