Putting a protective coating on the wood will make it last longer and make it significantly easier to clean. Poo has a tendency to stick REALLY HARD to bare wood and will require scraping, yet will wipe away with spritzed water if the surface is painted.
I painted the plywood interior on my coop. Two coats of oil-based primer and 3 coats of exterior semi-gloss. Walls and floor. If you prefer the natural wood look, I recommend linseed oil mixed 50/50 with mineral spirits. The oil will give is some waterproofing while the spirits will help it absorb into the wood. It's probably a little high on the toxic level, but would be dry and odor free within a day or so.