Natalia.
Do you honestly think that if any black ops or outside government organization knew about any of this it wouldn't have at least one person on the inside reporting back from the jump? I am not saying that Shield was ever overly competent, that's not going to be argued as we both know it wasn't, but if there was a Fury, if there was a Stark with any kind of ties to get the over-all sweeping done that would need to be done to find these anomalies, don't you think it'd have happened before the numbers got as big as they have? Hell, they knew about Wakanda, they all knew about the 'school' in Westchester or whatever the hell it was, they knew about Madripoor, even if they weren't especially good at what they did in the long run, they at least knew where to look.