considering that none of of us have seen one in atmospheric flight, we don't know. It would seem to me though that they are also used to provide aerial support to ground troops, and it may be during this time that VNE's are actually used. They would also help to stabilize a craft. Couple these with reaction control valves and retractable mobile canards, you may find the answer there. Basically a combination of existing technologies. The VNE's from the harrier and the F-35. The canards date back to the 80's on an f-16 AFTI (they allowed the ship to rotate on its Z axis), and the reaction control valves which replace the need for the tail assembly (see switchblade).
Whether you agree or not, i see atmospheric flight in FS2 wingless craft as a combination of things, not just one technology making it happen.