It sounds unsafe once all the information collected on those millions of people is placed in a central location and then hacked by or leaked to a nation-state level adversary.
If you said that 99% of them don't actually have power or access, it could be true, but irrelevant if an adversary has essentially 100% and unlimited resources to review them and double check the work.
>the clearance is only a confirmation that nothing is wrong in your background
In theory. The security clearance investigators are not perfect, and moreover, it's been publicly reported that sometimes contractors have falsified records showing they performed investigations. Statistically, X% are going to be flawed.
If an adversary has ~100% of the records, then think what they can do by reviewing them. Compromising someone doesn't require an earthshattering discovery because the cardinal sin is failure to disclose.
Let's say, for example, a person smoked pot a few times. From what I've read, that's generally not a big deal as long as you aren't doing it currently and don't lie about your history.
(The DOE rule seems to be that if you haven't used illegal drugs for two years, then they're not disqualifying per se, depending on a holistic look at a person)
But if an adversary has the entire investigation and every other piece of information that the federal government has on every employee, and they can determine that a given person did in fact conceal anything, then it is leverage to compromise them. Do X or you will be exposed as having lied. Or even "do X or you will be framed as having lied". It could be just enough to get someone to perform some action that further compromises them, and so on.
The more people this is done to, the more it snowballs. They could say "this higher up person works for us, so if you don't cooperate they will help us frame you for X". And it could be true, so how can a person verify?
If they have everyone's investigation, then all of the people who do have access to important things are at risk, and anyone who is truly spotless cannot be sure who is compromised.
Ancillary information like fingerprints makes it even worse, as all covert agents anywhere can in principle be detected and eliminated. This type of apocalypse being quiet, an absence of reporting on it wouldn't be evidence against.
I deduce that the whole scenario likely happened starting several years ago, based on public information, summarized at:
https://en.wikipedia.org/wiki/Office_of_Personnel_Management...
I am not making a categorical statement that seeking a cleared federal position is a mistake, but consider the gravity of the decision to trust the system if you do.