The key to reducing aero drag in the cooling system is to have a smoothly ducted system, and have the intakes in a high pressure zone (like the very nose) and have the exhaust in a low pressure zone (like the rear fascia of the Kamm back).
Look at the Britten V1100 for the potential of a fully ducted cooling system:
Neil Blanchard Designs: Britten V1000/V1100 - The Most Innovative Motorcycle Ever?
The radiator is under the seat, in the tail section. The intake is the 2 small oval opening on the nose of the fairing, and the exhaust is the "stinger" tube on the very tail. This worked perfectly to cool a 160+HP v-twin race motorcycle. A really fast, amazing motorcycle.