I've had homemade wheel covers on for a couple months, and haven't noticed any adverse braking effects. The only thing I've noticed is a ton of brake dust on the inside of the wheel cover when I take it off.
Actually, about 2 weeks ago, the lug nuts came loose on one of my wheels...the tire is also losing a lot of air, so I'm not really sure what the cause of the problem was on that one. It was probably due to the lugs not being tightened enough the last time I tightened them, and they eventually loosened, causing the tire to wobble around too much and lose air.
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