I haven't had a deep layer of algae either. I know in actively aerated hydroponic systems where the surface of the substrate is very wet all the time, they can sometimes multiply to form an thick green slime layer if there is not a cap over the top of the substrate to block the light, but no issues like that with a passive system.
They are not only harmless to plants, but they can be beneficial also. They photosynthesize their own food and release oxygen into the media. When they die, they are food for other organisms which adds organic matter and nutrients. Where there is some moisture and light there will be algae. They grow on the white vinyl siding of my house too, which bothers my wife.
