I've not used one of the Wheelbuilder.com covers, but I've never heard anything bad. They are a tad heavy, but certainly are very aerodynamic. I would say that aerodynamically, you would not notice much difference between the cover and a disc. Kraig Willet has a paper where he tests the cover vs. a disc on BikeTechReview. I think it is like $15...
I would say the only reason for any differences in aerodynamics would be from the junction between the cover and the wheel. I would guess this would be similar to the findings Zipp posts for the lip on a clincher rim vs a tubular, which is like <5 watts or so at 30mph, but that is just a guess. A wheelcover is going to be faster than any other wheel (except a disc) in terms of aerodynamics.
It would be nice to have one since then you could train on a disc and get used to the handling, without worrying about cracking up an expensive race wheel.
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