Once you enter Shimano’s world of carbon tubulars, you’ll need to have an intimate friendship with the Shimano Dura-Ace BR-9000 Carbon Brake Pads as well. Shimano designed its carbon-rimmed wheels to have a braking surface that would work exceptionally well with their BR-9000 Carbon Brake Pads, something they were especially keen to accomplish since the braking quality of any carbon wheel is always a primary concern. Sticking with the intended hand-in-glove feel of the Shimano wheels with the BR-9000 Carbon Brake Pads will keep you safe. They are designed to resist the frictional heat that you get from carbon braking. If you use any other pads on a Shimano carbon tubular, then you will unwisely void the warranty in addition to reducing the braking performance.
The BR-9000 Carbon Brake Pads are made from a proprietary compound that has been engineered to work with Shimano carbon wheels. You should not use these with your alu rims because the braking will be compromised and you will damage the pads. Similarly, Shimano has developed the pads to work with their own products, and so they cannot endorse using the pads with other manufacturer's wheels. But if you set up the Shimano Dura-Ace BR-9000 Carbon Brake Pads properly with a pair of the WH-9000-C24 or the WH-9000-C35 Carbon Tubular Wheelsets, then you will be once and for all convinced that carbon not only brakes as well as alloy rims, but there is an exponential improvement in the overall ride quality.