I reckon it's misdirection. "We'll say it's a UFO, but really it's a hypersonic plane in development." Just like the SR71 had a cover story during its development phase. "The wreckage was recovered in two days, and persons at the scene were identified and requested to sign secrecy agreements. A cover story for the press described the accident as occurring to a F-105, and it is still listed in this way on official rec…
Its probably a system for "jamming" FLIR sensors an allowing the attacker to project targets onto the system. The pilots were guinea pigs. Which is made more plausible by the fact that the USS Princeton asked the Nimitz pilots first if they were armed, and only after they informed the Princeton that they were not that they were given the orders to investigate. There probably was a real object -- since one was sighted…
If the Navy had told the pilots, "You just experienced an advanced technology test. Nothing to worry about" then they would have undoubtedly kept their mouths shut and not talked to the media.