Hi. Welcome to the forums!
I also have a biocube 29g. I have taken out the bioballs and added a fuge and a media basket so I no longer use the filter, BUT in my opinion I think you should continue to use it and change it, it can catch particulate matter before it goes into the next compartment.
Water changes are necessary whether the tank looks like it needs it or not. Trace minerals are used up by your corals and they need to be replenished via new water as well as taking out the nitrates.