Doesn't SETI boggle your mind?

Anyone who remembers Howard Hughes' Glomar Explorer, which was used as a cover story by the CIA to recover a Soviet submarine sunken in abyssal waters, has got to scratch his head over the sprawling SETI project currently listening to the stars. Who's paying for all this stuff?

Is SETI a cover story, too? A sleight of hand, a bit of misdirection? If SETI is the bumblefutz public version of "communication with E.T.," what and where, pray tell, is the quietly out-of-sight version? Thule? Neutrino research labs buried in salt mines? Area 51? Hmmmm...