Yeah, brakes need cooling, but hypermilers with a manual transmission will barely need brake cooling. I did the math for my Subaru a while back, and if I were to panic stop from the car's theoretical top speed of 120mph, and the heat were evenly distributed throughout only the brake rotors, the temperature rise would be only half of what's required to boil brake fluid. From 85mph->0mph dissipates half as much energy as 120mph->0mph. So a single panic stop doesn't require brake cooling, since you have enough thermal capacitance to prevent overheating.
Repeated application of the brakes is another story, but hypermilers don't do that, unless they're descending a hill with an automatic transmission.
Smooth wheel covers completely block the flow from the inside to the outside of the wheel, but what can you do to reduce flow across the inside of the wheel? Coroplast mounted to the non-rotating side of your hubs? Whatever you do, make sure it doesn't get caught on something and end up tearing a CV boot or brake hose. I file this under "would help slightly, but probably not worth doing."
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