The least-cost conspiracy theory here, is that 'project aurora' type developments sometimes lead to aircraft with unexpected flight patterns and low radar visibility, so the Navy is basically saying 'we don't want to reveal we couldn't detect this, and it was inside a risk window for our defence ring' along with 'this tech exists, but we don't want to say so or confirm'

The second least-cost conspiracy is that like 'Corona' with the NSA and donation to NASA, revealing original quality material informs hostile entities of the resolution of current detection and recording devices in ways the Navy do not wish to reveal, since it will alter the advantage in imaging and detection. This is almost the inverse of above: they did detect it, thats revealing in ways they don't want people to know.

The most expensive-cost conspiracy (i.e. what i feel is the least likely to survive occam's razor) is "Aliens"