Come on, the government can't do anything efficiently. It beggars credulity that it could keep a secret perfectly for decades.
Especially since we're talking about multiple governments, multiple factions coming into and out of power. Politicians like nothing more than to expose the scandals of their opposition or predecessors, and reporters want nothing more than to expose the next big government scandal and be the next Woodward and Bernstein. The level of scrutiny in Washington is therefore monumental. And with so many people who'd have to be involved in a coverup, that makes for a lot of lines of communication that can be intercepted, a lot of weak links that can be exploited, a lot of chances for people within the coverup to decide that it's wrong and needs to be exposed. The bigger a conspiracy gets, the exponentially more improbable it becomes that it can be kept secret indefinitely.
So as a rule, the only secrets that ever get kept in Washington are those that everyone agrees it's in the interests of national security to keep. The Stargate franchise notwithstanding, I don't believe the existence of saucer men from Koosbane is such a secret. On the contrary, if people from the opposition party found that the sitting administration had knowingly conspired to cover up the existence of skinny grey alien nudists who were abducting American citizens for titillatingly invasive and generally pointless probing, they wouldn't agree to keep the secret; on the contrary, they'd make a huge scandal out of it in order to blow away the opposition and retake the White House.