Plugging that vent upsets the design of things. One, it equalizes the air pressure behind the fairing. With it plugged you create a vacuum going down the highway. With it open, the wind moving upwards behind the windshield from the vent is moving faster than the air in front. It pushes the air higher as it comes over the windshield making for less turbulence.
This past Sunday I rode through a lot of light rain coming home from the CBR. At one stop, I put a rag in the vent scoop. A few miles down the road, I pulled over and took it out. Dealing with the rain coming through that vent was better than the alternative.
So, pull the plug and put the shield back on. If you don't already have a pair of fork deflectors, they help a bunch with all the wind coming up in front of the tank.
http://www.bigbikethings.com/winddeflectors.html