The biowheel, like bioballs, is NOT a nitrate factory.
It is very efficient at the conversion of ammonia to nitrite to nitrate due to the ability to foster the growth of aerobic bacteria.
It may not be necessary, but nitrate problems exist for a variety of reasons. If you have these reasons, you can blame the wheel all you want, but it isn't its fault
1) Overstocking/overfeeding - what do you have, how often and what do you feed?
2) Export mechanisms - how often and how much do you change water? How often do you remove macroalgae from your system? How effective is your skimmer.
3) Janitorial staff - healthy sand bed and clean up crew.
If you overfeed, overstock, etc you can be doing everything "right" and still have nitrate problems. So it is important to eliminate other sources. I don't personally think you will have an issue removing the wheels, but it may not really be the source of your problems.