The reputation that some forms of filtration have attained as being "nitrate factories" is somewhat of a semantic argument IMO. Sure, these methods can work, but they are by no means the "best" way to go. Just about any system, including no filtration (ie. daily water changes) can be made to work with enough effort - that doesn't make it a good idea IMO. It really depends on what you're trying to achieve in terms of water quality and what sort of maintenance you're willing to perform.
Any type of filtration that provides an area or media that can potentially trap uneaten food, detritus, etc. which can then decompose and degrade water quality over time can potentially pose water quality issues. This goes for canister filters, undergravel filters, hang-on power filters, bioballs, sponge filters etc. Sure, if you maintain these devices diligently enough this won't be an issue and they can work fine, but why would you willingly setup a system that requires more maintenance when there are better, more natural and lower maintenance alternatives?
I guess I don't understand why anyone would want bioballs in a modern reef system...