I can see your problem. Can you stack those smaller ones to give you a smaller area to cover? I think those little ones are about 12" or maybe 14" cubes, somewhere in that range. The big ones maybe 16"? Whether you can stack them or not, they should be less than 8' long as they are pictured. So you can do it with less than a half sheet of plywood.
First thought is to cut plywood to just lay on top of those crates. The chickens should still use the nests. As long as you cut them to fit with no overhang they should stay. If you make them too big so you have overhang the chickens might walk on them and flip them off. I don't think the poop will build up very fast. If you need to clean them off, just pick them up. About as simple as it gets.
Another thought, which I don't like as much, is to make a table on top of the nests. Cut a piece of plywood wide enough to cover the widest nest and maybe 8' long. Use those two pieces of 2x4 on the wall to support the back edge, they look to be the same height. Screw the plywood to those 2x4's. Put a couple of legs on the other two corners. To make the legs I'd cut a length of 2x4 the right length and stand it under the plywood. Put a couple of screws through the plywood into the 2x4's. With those legs it will not be very strong but it doesn't have to be.
Good luck with it.
