It's probably a good idea, although you may want to do it in stages, like remove 25% of the bioballs, wait a week, make sure there's no ammonia, repeat, etc. Most current reefkeepers don't like bioballs because a tank relying totally on them for biofiltration has no areas of lower O2 concentration that allow different species of bacteria to thrive. These bacteria that need low oxygen habitat are responsible for processing nitrate into free nitrogen. Typically they live in a 4" deep sand bed, although there are opinions that they also can colonize areas of live rock.

You already have alot of live rock, so removing the bioballs might not change much. The bioballs themselves do not "produce nitrates" they just don't provide the habitat for low O2 bacteria. They're not preventing it from growing in your sand or rock as it is now.