It's not actually secret I think. It's just that a massive supermajority of the population practices willful ignorance because the supernatural is farking terrifying. Everybody's had some encounter they try to forget.
Yeah, as a general rule in nWoD there's no massive top-down conspiracy enforcing a party line and what massive conspiracies there are a. still tend to be pretty limited in the slice of the world they can actually engage with (since they're multinational corporations or shadowy government agencies or something that's neither but kinda wearing the skin of both vs Vampire World Government) and b. dealing with deliberately watered down versions of the other splats that they can meaningfully engage with instead of, like, "the Changeling lunges across a threshold and pops into the Hedge and is five states away by dawn"/"the werewolf pack goes furry warframe on your ass"/"the Mage makes your liver explode last Saturday" (moderate exaggerations for illustration, but on the whole I'm pretty positive of the idea of rewriting versions of the other PC lines that are explicitly meant to function as antagonists, threats, and uneasy allies at best for Hunters, but that's sort of a tangent).
Everything is, generally speaking, pretty fragmented afaik. The highest authority in Vampire Land is the Prince fr'ex, the ruler of a single city (sometimes not even that), and they don't have the resources or power or incentives, necessarily, to run a perfect clean up operation. Mages are concerned about not being seen but that's because Paradox is a bitch and sometimes it brings brainspiders, and it's notable that this barrier is pretty malleable and movable depending on how motivated (or moral) you are. Changeling Courts care more about hiding from their Keepers than about hiding from humans. And so on.
I like it tbh. It's less Sunnydale on steroids imo and more...in nWoD there's a whole different world waiting there in the shadows and the depths and the lonely corners of the Earth. It's there and once you see it it sees you and it's so, so easy for even normal people to fall through the cracks. To be lost in it and never find your way back. It's less Enforced Dogma and more, like you said, many people, maybe even most people, have seen something that doesn't quite make sense. That they've uneasily dismissed and tried to forget but still think about sometimes, when they're alone in the dark.
And I love that mood really.