Query

The algae could, in theory, block sites for the bacteria. Also the filter bacteria grow better in the dark, one reason they grow mainly in the filter as most filters have their media tucked inside a nice dark box.
Is there any way you could rig a cover for the filter? Something loose fitting but would stop the light shining in? That would reduce algae growth and make it darker for the bacteria. But not something that would melt in the heat from the lights....

Yes the algae would act like any other plant in the filter, it's the blocking of the media so the bacteria can't get a good hold that would worry me. It may not do that, of course, it may be just me worrying needlessly. I just don't like the idea of algae in my filter