Yes. If you are using crushed coral, you need to vacuum it. If it's too deep you can't vacuum it.
The more complete answer is that you probably shouldn't have crushed coral in the first place, and should convert to a deep sand bed. You probably cannot make a DSB too deep. I've heard of sand beds in sumps up to twelve inches deep.
Agreed, there is very little benefit of having a deep bed of crushed coral. It won't give you denitrification benefits and its a detrius trap. Because of the latter, as reeflion mentioned, you need to vacuum it. I'd recommend a python as a good tool to make this easier. However, the best bet is just to remove the excess substrate and keep 1" or less. Or swap it out for oolitic sand (<.5mm). Detrius can't penetrate the sufrace, the surface area for bacteria is gigantic, its anaerobic thus supports denitifying bacteria, its the best substrate to support sand fauna, and it just plain looks cool. For more info check out http://rshimek.com/reef/sediment.htm
