When I change the water I vacuum the sand bed out. I stuck a rigid tube on the end of the siphon hose. It's pretty gross what comes out of there. None of my sand dwellers mind, snails, wrasse, goby. If you are trying to have a functional deep sand bed over 3 inches I wouldn't do it, but if you have less than that I think it's a really great way to keep the tank healthy by getting poop and leftover food out of there rather than letting it break down into nitrates and phosphate and then getting them out of the water. For me there's plenty of bacteria inside the rocks, and I guess I have enough "microorganisms"
PS I also use a turkey baster to blow off the rocks before I vacuum. A lot of gross stuff comes out of there too. Also, I think it's good to do from the beginning, if you let a lot of nastiness build up in there you have to be careful about stirring it up