Having ridden into the wind on both, I would say that even riding on the hoods or tops is more aerodynamic than riding a flat bar bike. My guess is that most flat bars are still wider than riding on the hoods so you have a wider profile against the wind...I don't know really, I just know it feels like I'm getting hit by more wind with flat bars, and can tell the difference between riding in regular position on flat bars and riding with my hands much closer to the stem (away from the brakes).

I mean...I can only tell when riding into a headwind. :-) Just sayin'...