Linoleum or something similar over your wooden floor would be easiest to clean but wouldn't let the wood "breathe" and could cause rot quicker in a damp environment. Painting the wood with a gloss finish exterior paint would still be easier to clean than bare wood but would eventually stain with poop or whatever, over time. I assume you are talking about a plywood floor.
How high off the ground is your coop area?
That wouldn't leave a whole lot of room underneath for circulation then either. Unless you were stacking them 2 high. I would probably go with the paint idea, simply because I would worry the ground moisture would rot the flooring if it were covered with plastic. We live in a very wet, humid environment here.