There ain't no reason why the Navy should do this. Not denying that they did, but until the DoN has a solid grasp on what this is, whether real or a Radar phenomena, it should not be reported. There are just too many hysterical conspiracy theorists out there that will attach themselves to this and cause problems for the DoD.
There is a lot of experimental activity going on all the time, a lot of it classified. I suspect that these very infrequent 'encounters' are not the same thing but chance encounters with different activities. A hypersonic vehicle may show up on radar, but its not something a hornet driver is "almost going to hit". Two different things.
When I fly I regularly (as in about once a year) have near encounters with things varying from weather balloons to Mylar birthday balloons.