I can see how a bare bottom tank is easier to "keep clean". Any detritus is easily syphoned out of the tank and high flow can be maintained. This could be good for sps corals so long as they are well fed. There is less chance of having lots of particulate matter floating in the water column, so that the water looks clean and scrubbed. People may argue that it is also easier to maintain stable water parameters as there are no dead spots where ammonia, nitrates and phosphates can build up. Many people may also prefer the aesthetics of a bare bottom. Tank that is!!
Personally, I want my little reef to look and operate as naturally as possible. I feel that a mature sand bed helps to keep the water clean. It is a massive base for beneficial bacteria to develop, thus maintaining the nitrogen cycle. The sand is also home to many creatures who very kindly feed on all of the detritus produced in the reef tank. In turn this population of minibeasts provides food for many fish and corals in the tank.
According to Ron Shimek, a noted biologist who has written a number of articles on deep sand beds, hydrogen sulphide will not leach up out of the sand bed and poison the tank. He also believes that manual sifting or cleaning is not necessary to control detritus accumulation. A good sand sifting crew will do the job. A wide selection of snails, conches and crabs will keep the sand sifted and aerated.
Many fish and other creatures which we may wish to keep are also dependant to some extent on having a sand bed. I have a love of wrasse, many of which depend on a sand bed for their nightly refuge. Survival of these wrasse is often questionable in a bare bottom tank.
I love having a complex and pretty natural ecosystem and believe that it is pretty self regulating so long as I don't mess with it too much. I like the wide variety of creatures and organisms living in my little reef. I also believe that my sand bed is critical to the long term success of my Macropharyngodon and Halichoeres wrasse. The sand provides them with their natural place to sleep and also gives them a constant supply of little critters to supplement their diet.