I think it's a good idea. Just make sure it easily removes for access/cleaning. Keep an eye on the one for the overflow that it doesn't get too much algae or a sheet of nori blocking the flow. I'm doing one of those myself. I'm torn between the open crate or a black top cover. On my last tank I had a piece of cardboard blocking the light and after I installed it I had to keep an eye out at first for stuff dying off and blocking the pipes but it obviously was stopping some stuff from growing. On this tank I have the small drain hole (3/4) w/o a pipe and when the main pump is off it drains the box at feeding time so I think I may not have to worry about as much growing anyway. But,,,??
If you put it over the whole top you will lose light intensity though so I would leave it with just your overflow and back.