I don't pay close attention to the way HN does these things, but I recall that NSA was one of the terms that the HN moderators chose to penalize. Or they could have manually penalized it as well.
HN is a sandbox that YC created for folks to play in. Their sandbox, their rules. I'm not criticizing you for complaining about the Intercept article being buried on the fourth page or whatnot (I would have more liberal rules if it were my sandbox), but merely saying it's probably not that productive to complain about theirs.