bio balls won't create nitrates.
are you keeping live rock in your display to hold bacteria? if so, you can completely remove the bio balls if you like.
if not, i'd suggest leaving them right where they are.
if you have live rock in your display, and bio balls in your wet/dry that are loaded up with detrius, and losing the battle with the bio load, you can simply remove some and rinse them in saltwater, and return them to the wet dry.
i would not keep anything in the system that works against it's overall health.
as for your macroalgae theory, i don't think the algae would export enough nutrients to not notice the presence.