There are absolutely builds where a bare bottom would be preferable (tanks with lots of messy carnivorous eaters, tanks that need extremely high flow, and frag tanks all come to mind), but for an average reef display tank, I don't see that it provides any benefit. Sand sifting/cleaning/suctioning is definitely a necessary part of tank maintenance just as water changes are necessary to promote a healthy water column, but substrate provides a home for benthic organisms, a stabilizing base for live rock structures, and is quite pleasing aesthetically.