Live rock is better bioballs become nitrate factories. However in a reef aquarium the nitrogen cycle usually stops at nitrate. Anaerobic bacteria need low oxygen environment to convert nitrate to nitrogen gas which does not happen on a large enough scale in a reef tank to keep nitrates in check. Nitrates are controlled through water changes and proper maintenance in a reef aquarium.
Protein skimmer help by removing organics from the water before they have a change to break down into nutrients such as nitrate and phosphate. So protein skimmers dont remove nitrate but they do remove many organics before they can become nitrate.
29g Mixed Reef, 150w 14k Phoenix MH w/ Moonlights, Reef Octopus BH1000 HOB Skimmer, Ecotech Vortech MP10es, ReefKeeper Lite (Plus), PH Probe, Temp Probe, ATO, Carbon/GFO Reactor.