I ran my tank barebottom for the first year. While it does make it easier to maintain the tank with detritus removal, I did have a few problems. As corals grew, it became apparent that one day I would not be able to fully clean the tank around the rock structure because of coral growth. I added a one inch sand bed and am very happy.
Also, in a barebottom system it is even more important to get the detritus out of the tank. I have 4 MP40's and an Iwaki 30 Return pump and still had spots where detritus would accumulate. I don't care how much flow you have, the bottom of a barebottom system will never look totally clean. Also, as your corals grow it becomes that much more difficult to reach all these spots.