More to the point, they don't (presumably) have some secret pipeline of highly talented people. I mean, the pool of graduates in mathematics, statistics, computer science, etc., year in and year out, is available to everyone, NSA, other public sector, other private sector, etc. And while the NSA probably prioritizes hiring brilliant math wonks and what-not, so do wall street hedge fund companies, tech companies, etc. And given that at least some small percentage of "really smart people" would probably refuse to work for the NSA just on ideological grounds, I don't see any reason to believe that they have a monopoly on smart people who can do crypto research and what-not.
As for their financing, however... I don't know. I'm not real big on conspiracy theories, but I don't doubt the existence of secret budgets and "off the books" stuff to fund certain government programs. I mean, just go back to the Iran/Contra affair[1] and you can see that some sneaky stuff does go on, at least on occasion.
[1]: http://en.wikipedia.org/wiki/Iran%E2%80%93Contra_affair