I vaguely recall an article in AFM, I think, where some one looked at that. If you use ORP as a measure of success, the bare bottom was vastly superior, as he was able to maintain an ORP over 25% higher in the bare bottom tank. During the course of the experiment, it didn't really seem to matter, though. Both tank did just as well, no obvious difference in livestock health.
The only thing is, I really don't like the look of a bare bottom tank. Personally, I much prefer the appearance of at least some sand on the bottom. Looks much more natural to me.