I think you're a bit confused. Bioballs, or other neutral media, do not "gather" nitrates. They simply provide areas for nitrate to be produced. As I see it, there are two reasons why bioballs are both unneeded and unwanted. To understand these reasons you must first recognize what bioballs do. All they do is provide extra surface area for aerobic bacteria to grow. Aerobic bacteria converts ammonia to nitrite to nitrate. The reasons we don't need/want them in our reef systems are:
1. We don't need them because most any setup system has far more than enough surface area for sufficient aerobic nitrification. The only way you'd possibly need something extra beyond the liverock, sand, and other surfaces on the typical system is if you had a huge fishload. I could only see the most awful setups where the person crams so many fish without regard actually needing bioballs.
2. We don't want bioballs in reef systems because they lack one major component, anaerobic denitrification. They do not have areas of low oxygen where nitrate can be converted to nitrogen gas. It has been observed that anaerobic denitrification occurs most efficiently right next to zones of aerobic nitrification. So the net effect is that a tank with only live rock (which has areas for nitrification and denitrification) will not have the nitrate problem of a tank with live rock and bioballs.
Bioballs are not alone in this. Most mechanical filtration (sponges, floss, etc) can provide places for excess nitrate production. I don't really know about whether carbon does this, but I suspect that it does not suffer from the problem nearly as much as bioballs and mechanical filters. This is primarily a guess on my part. Seeing as how carbon has many beneficial properties (compared with none in bioballs), I don't think it is worth second guessing using it. Also, from experience in running carbon, I have not seen any problems with it elevating nitrate.
