If we're dealing in the comic universe, and arguing from the viewpoint of those trapped inside, the justification that all databases WILL be compromised requires 4th wall perspective that only a select few characters have.
Really, the idea that super-villains will always be able to defeat anything the super-heroes can cobble up has little support within the universe, because the heroes constantly win against ludicrously slim odds...and do so with ridiculous regularity. They laugh while leaping into their apparent doom because they'll survive largely unscathed as they have many many times before. Their bravado has been supported by experience. From the viewpoint of the superheroes within that universe, It's just as feasible for the superheroes to cobble up insane security measures that could not conceivably be broken by any entity interested in earthly affairs. It's only the readers like you and I that know that comic authors only detail the complexity and robustness of a security system only to have it breached shortly afterward. But for the heroes, that's not a factor they can conceive, and it shouldn't be influencing their opinion on the matter unless they have 4th wall perspective.
For example, pick any superhero with a secret known by someone other than themselves, or documented outside of their own mind. The fact that secrets still exist in that universe shows that they can indeed be preserved. Even Spiderman's identify after being made public, was made secret again. The mutant registration act could just as easily succeed as it could fail. And given the heroes vs. villain track record, it should lean heavily in the direction of success from the viewpoint of the heroes. Hell, it's being pushed by the illuminati, masters of science, technology, magic, heck, reality itself was subject to their will.
If we want to go really really meta, then we should know that we'd never have the secret identify of every marvel superhero revealed to the world because it would derail far too many character arcs and make for bad reading. Leaks would be limited at best to C and D-level characters, or somehow retconned if it somehow happened to major characters.