There isn’t a best substrate for reef keeping. I’ve kept BB and sand tanks. There are advantages to both, but with the advancement of nutrient exporting either will work well. Personally in reason years I have kept the sand bottom for two reasons…firstly for me it’s aesthetically pleasing and secondly it’s a must for the many sand burrowing species of wrasses I enjoying keeping.
Functionally, I went with bare bottom with just a cosmetic <1/2 inch layer of sand, easy to keep clean, no sand blowing around, no nutrient sink. Snails could travel around easily, on the glass bottom.
I also kept (Florida crush coral #5) a gravel bed in my sump for ricordea farming and I found that some of my fish, (I started keeping gobies and dragonettes), were growing fat in the sump, but not in the main display. I found that copepods and amphipods can colonize a gravel bed, so now I have a half inch of sand/gravel in the main tank.
I've never gone bare-bottom but I am considering it for a small nano reef in my office to simplify maintenance.
I started my first saltwater/reef aquarium in 2007. It was in my office on my desk at work. It had a deep sand bed (2+ inches), the grain size was very fine, and it was live sand variety of some sort by CaribSea.
Later, I started a mixed reef at home. I used less sand because I thought a shallower sand bed looked more appealing from the outside. I had a mix of grain sizes. Overall I would describe the sand as much more "pebbley" (not a real word, I know) than the substrate in my first tank. This time I used a mix of CaribSea dry sands.
Although both systems were successful, I had a lot less cyano and algae issues in the first aquarium. I also used real live rock and water from the ocean in that system vs. dry manmade rock by CaribSea and the water I mixed inside my garage in a Brute trash can.
Aesthetically, I much prefer the look of an aquarium with sand. I think a tank without sand looks unnatural. However, with a wife and two kids competing for my attention--in addition to our other pets and schedule full of activities--I think I'm going to give this bare-bottom thing a try. I figure my home office is a good testing ground. It's not out in my entry where my main display is, so no visitors can judge my aquascaping sensibilities. I presume it will be easier to maintain since I won't need to siphon the sand to remove detritus. My hope is that it mostly stays suspended so it can be removed via filtration.
Other than how the tank looks from the outside is how it functions biologically on the inside. I know Ryan @ BRS had issues with his new tank that "magically" seemed to clear up once he added sand. Losing some of that biological filter through an absence of sand is making me seriously consider running a small reactor with bio-media in it to compensate. A side benefit to that would be that I could use that reactor to jumpstart future systems rather than the way I have traditionally, which was to use a sponge or bio cubes or ceramic media or whatever I had available at the time.