I have a shallow sand bed with approx 1" of sand and my reef tank is doing ok. I think you can keep a good reef with sand. I would take out sand in increments and see if your overall environment improves. Sucking out all the sand seems like an extreme measure to me and may cause more harm if you do it too quickly.

I siphoned mine out with each water change. I have less microfauna without the sandbed though. I had buttloads of little critters before I removed it, and now I don't notice any. There's a little in the sump, but not much.

The BB is much easier to maintain though, and I was also having the clumped sand syndrome, since my opened top won't keep any gobies in.

I slowly sucked out most of the sand in my old tank. Nothing died, but it was messy business. You won't believe the crud in a DSB! Lots of "shedding" from my live rock for about 2 months afterward. If you like the look of BB go BB, if you like the look of sand run a 1/2" to 1" and siphon and stir it. A shallow sand bed can be kept almost as clean as BB.