The ending of Vampire: The Masquerade Revised had a lengthy metaplot about the Sabbat engaging in terrorist attacks all over the East Coast of the United States, including Washington D.C. They used Masquerade-breaking flesh-crafted monsters, powers, and more. While this was Rule of Cool in the early tens, is it really surprising the government figured out vampires existed after this?
The Camarilla (sourcebook) uses material from The Hunters Hunted, Project: Twilight, and The Hunters Hunted II to explain that the government has been gradually piecing together things since the early nineties. Each edition has shown them get progressively more on-the-ball.
The cyclical Gehenna seems like an Ass Pull to explain why the apocalypse was cancelled. However, if the Antediluvians have been rising and siring childer for 13,000 years then why would now be any different? They can chow down on enough of their childer to satiate themselves then move on.
Why did the Lasombra defect to the Camarilla? Well, it's only half the Lasombra and that's chiefly because they found out their Antediluvian was alive. The Sabbat had completely failed in the one task they had been appointed themselves in doing and were running suicidally into the jaws of monsters. The Sabbat's lower ranks were also not developing the previous generations' refinement and planned on devouring their Elders in the sect too. Combine that with the Second Inquisition breathing down their necks and it makes sense the Lasombra moderates decided to get the hell out of the sect.
I can’t help but think of all the blood shed in Africa and the Middle East for this Gehenna Crusade, all the Cainite lives lost, of how we celebrated the one in twenty vampires who returned from conflict with a Methuselah, bloated like a tick on new power. We just forgot the nineteen fallen and where their vitae went. Who it fed. Who or what the ashes of Methuselahs summoned to the surface.—Lasombra Elder
Why are the Sabbat now so feral? Well, they've had a lot of their leadership defect to the other sects or killed by the Second Inquisition. The Sabbat can always make more shovelheads and indoctrinate them into their insane religion but it's a lot harder to make Elders or Ancilla.
Given the Second Inquisition includes thousands of soldiers, analysts, and operatives — it's going to be incredibly hard to put the genie back in the bottle of vampires existing. All it takes is a few of those people to start leaking the existence of the undead to the public and it's game over for the undead.
The lack of significant information is somewhat justified in that higher-ups in the different intelligence organizations behind the Inquisition are keeping the cards very close to their chest, and the rank-and-file grunts and common personnel are only given the absolute minimum of information at best. They especially kept in the dark about what exactly it is they are hunting, and are certainly not told that their targets are supernatural in nature; the cover story, that most of them believe (or maybe even choose to believe in some cases), is that what they are doing is coordinated strikes against "terrorists" and similar acceptable targets. The word "vampire" is not used in official briefings. Instead, the agents speak of "blankbodies", referring to the low body temperature of the undead that marks them as inhuman.
They also might count on vampires stopping existing relatively soon.
The appearance of a 16th generation implies that the Curse of Caine is evolving.
Gehenna isn't cancelled as many would like to believe, instead it's much slower of a reveal, namely V5 fits within the Crucible of God Module from the Gehenna splat. To list off everything:
Kine are aware Kindred exist, just instead of the whole of them it's the ABC organizations + the Vatican, who in response have re-canonized the society of Leopold.
Antediluvians are awakening and while none have declared their desire for godhood, it's already a big deal they're awake.
Thin-Bloods/Duskborn are now so numerous they are considered an accepted part of Kindred society instead of a dirty little secret.
