It probably does reduce total amount of braking force, but things like weight distribution, tire construction and rubber compound probably are more important factors. I didn't think the front brakes on the 900 Custom felt all that different than the front brakes on the 900 Classic, or any other mid-sized cruiser I've ridden.
The rear-heavy weight distribution limits braking effectiveness of the front tire, so even when there's a 17-inch radial and dual four-piston calipers with floating 310mm rotors on a cruiser it still doesn't feel like a sportbike's brakes, even if it does actually brake harder than a sportbike because of increased effectiveness of the back brake.
Racing tires are wider for heat dissipation and longer life. The tiny cruiser front tires will overheat more quickly. You also get more life from a wider tire or can use softer (more sticky) compunds to give you decent tire life with better traction.
For many materials, you're right that the contact surface area doesn't affect how much friction is available; the coefficient of friction and normal force are the only relavent parameters.
Tires are different though, as the rubber creates "micro-grips" with the road, effectively increasing the coefficient of frictions with increasing contact surface area. At least that's how it was explained to me...I'm a rocket scientist and not a tire expert so take that for what it's worth.
Ok I say MO should prove that theory. i.e that a heavy cruiser with less sticky tires can stop faster than lighter sportbike with sticky tires.... Maybe the ordinary rider can't stop quicker. But ask Matt Mladin which bike he would like to use in an emergency stop. Mladin is the only racer I trust to give an honest opinion. i.e. he cares less about saying the politically correct thing. I don't see how a Honda Shadow with rear drum and hard tires can outstop a modern 600 with double disks on the front and sticky tires. The limitation is the rider not the tool..