Good read here from Travelle Gaines, who runs a program that over 32 NFL players use in the offseason to stay in shape, and it basically sums up why he thinks conditioning tests are overrated.
Performance Gaines: What do conditioning tests really tell you? | Shutdown Corner - Yahoo! Sports
I don't think it's as cut and dry as whether or not teams should run conditioning tests, as I think it depends on what kind of team you have, but for me the interesting parts of the article are where he describes the kind of tests they do.