One of the things I like about a thin layer of substrate (such as sand) is it provides a bit of insurance in case of power outages, or pump failures.
The top layer ( to about a half inch in depth), will be colonized by millions more beneficial bacteria than on a bare bottom tank alone, so if for some reason a pump stops pumping water thru biomedia, this population in the sand, can pick up the slack.
It doesn't need to be deep.
There is only about 1/2" in the tank below, and beside holding that population of bacteria, I believe it also looks natural.
To me, bare bottom always looks artificial (and although I have kept bare bottom for a number of reasons such as fry grout tanks, etc ), for a display tank I would always want some substrate.
And because I mostly use PFS, the tiny interstitial spaces between grains don't really allow stuff to work its way in, like typical aquarium gravel does.
I also like using burrowing snails (like the MTS andyroo suggested) that live in the sand, keep it from compacting, eating any excess food, and helping to break down all organic material more readily available to beneficial bacteria.