(The same thing happened with the snowden leaks, BTW: it was suspected for a long time that the NSA or FBI had a survellance system similar to PRISM, because it's the kind of thing that they would want to do and have the means to do, even absent any concrete evidence of its existance. The leaks just confirmed the existance undeniably and also showed how extensive it was)
As to the other points, when some top secret info does get revealed, legally or not, and the public reaction is pretty much, ehh, we already assumed that -- that seems like a pretty big failing of the whole concept of "secret." And on the other hand, I'll grant you a few exceptions, like the names of spies, position of gear or troops, perhaps the detailed weapons specs like you mentioned -- but when the name of this system is "top secret" and seemingly well over 90% of what is marked "classified" lacks any informational value whatsoever, that's a failing in the other direction, people stop caring about "secret" because so little of it is actually important.