The reason for the brakes is aerodynamics. Less stuff stuck out in the wind. Also it's a bit more stylish, I suppose, for aero road bikes.

The ones that really changed things are the brakes that are integrated into the frame, meaning the frame or fork themselves have the calipers as part of their carbon layup. Using carbon they can make them flexible enough to be springy. They work the same but the arms are part of the frame or fork. I think Storck uses them, maybe Ridley.