Not really sure what category this should go in...

Anyway; today i took of two of the three mounts on our roof rack since I'll be the only one riding during the winter. I figured it would increase aerodynamics and stop potential wear on the mounts. Previously, we only had noise when bikes were on the rack.

One I too kit off and we were driving today, we noticed that there was a loud noise as if there was a bike on top even though there no was only one empty mount.

Has anyone had a similar problem?

This doesn't relate directly your question, but there's a LOT of drag from an empty roof rack. Mine costs me about 10 mpg on a Honda Civic with bikes up, but 3-4 even empty. I use it only once or twice a week in winter, and it's worthwhile just to flip the latches and lift it off in one piece between rides. I can put it on in about 2 minutes, take it off in less than one.

You'll get a lot of drag and wind noise with anything on your roof. I only put my rack on when I need it.
Btw, the fairing doesn't help nearly as much as they hype it to. There is some slight reduction, but the really the only reason I kept it was because it looks cool.

Edit: Just to give you an idea of drag:
I drove about 250 miles with a kayak on the roof of my 93 Accord. I got about 20 mpg hwy

Even behind there is drag from the turbulence of the air
passing around stuff back there.
increasing the frontal area , above the car, most definitely ..
Though slowing down helps ..