It is the same argument for bioballs. Biowheels themselves do not increase nitrate levels. They simply provide surface area for aerobic bacteria to colonize. They however do not provide an anaerobic environment that will allow nitrates to be converted to nitrogen gas. They also suffer from the same 'nitrate trap' problem as bioballs. I have 2 Emp 400's on my 55gal QT and I never realized it, but boy, the bottom of the filter was absolutely disgusting with detritus. The biowheels themselves can clog up with detritus and algae can form and block the biowheel from spinning.
In the real world, I will simply say that your Emp 400 isn't bad, so much that it simply isn't needed, esp. once you get that skimmer. If you keep the tank's bioload low enough, then your liverock/sand, coupled with water changes, will keep the tank's parameters in check.