There are no other lists of powered individuals other than SHIELD's secret encrypted index, and just becuase a shadowy spy organization with laughable levels of oversight got infiltrated by terrorists doesn't mean every authority is at risk of it.
And sometimes it turns out those authorities in fact are the bad guys. The good guys in S.H.I.E.L.D. and later the ATCU didn't know they were really doing HYDRA's work.
Which is why I don't like the position of unlimited trust without oversight SHIELD and the Cap seem to want. They tried that with SHIELD before and found it became a HYDRA front.
Seeing that scenario unfold not once but multiple times is what changed Coulson's perspective, it didn't come out of the blue.
Be nice if they had hinted at that before this episode.