In "Space Seed", Kirk said the disapperance of the Botany Bay was never in history texts (that would mean all the way into the 23rd century). Spock responded it was probably because it was thought a war-weary people would be frightened by the prospect of all those Napoleons out and about, somewhere.
So, a cover-up. A conspiracy on Earth and in the Federation to keep the truth from the people. It's just two throwaway lines between Kirk and Spock in the "Space Seed" story, but it is a major cover-up, nonetheless.
Now, the Botany Bay appears to a Federation that just lost Vulcan. The thinking? Cover it up. Eighty Napoleons being secretly held in stasis because the Federation is afraid to do anything else. So, you think you're safe? It's just an illusion.