What stage in the game are you? The best solution is a floor made of Applied Energistics Transition Planes. Any eggs that get spawned on the sewer will be lost, but at worst it would be a 1/25th of the eggs.
Another solution is a floor of hoppers, but chickens may occasionally fall through and die. Obsidian Pipes powered by redstone engines have a collection area of 3x3 blocks, much like transposers did, so a few of those on the roof would pickup most of them.