Algae has a hard time living with out light. No light = no algae. Algae itself isn't much of a problem. It can clog air stones and pumps, it can eat nutrients and mess with the PH, but it doesn't directly harm plants. Eventually it can attract fungus knats, which after a while can cause real problems, such as worms in your roots.
Dutch master Zone does a great job at discouraging algae and any other microbes, including beneficial ones. If you are running all chem nutes and no organics/bennies, then Zone is cheap, effective and a bottle lasts forever.