As you've determined, you won't be able to stir it. I don't use eggcrate myself, but regardless, I'm a believer in vacuuming out the sand and rinsing and replacing periodically, and you should be able to do that whether you have eggcrate or not. Stirring the sand can remove any gas bubbles but just stirs in the detritus. It won't necessarily all rise to the top of the sand for removal. I know that seems extreme, but I don't use a great deal of sand in my tanks. Unless you've got bower builders or some other reason, why go 2-3 inches deep?
I think most just don't stir what gets trapped in the eggcrate and report no problems from it. I'm sort of obsessive about removing detritus myself and that'd bug me.
