My coop floor is plywood which I covered with rolled vinyl flooring. It was about $10.00 for a 6x10 roll -purchased at a hardware store. I love it because it is easy to clean, and keeps spilled water from dampening the coop. Microfiber cloth I keep on hand soaks it right up with no damage.
My chicks were vaccinated only with the Mareks vaccine. We are trying to raise them as organic as possible. Therefore in order to avoid coccidiosis without medicated feed, we allowed them to build natural immunities by not sterilizing the coop once they were moved in.
We use a 2-3 inch layer of pine shavings, and add more on top of that every week. I allow the coop to get plenty of air to make sure that their droppings dry. After a couple of months of going from brooder to coop I cleaned out the old shavings (My coop floor is 6x8 with 8 chickens which I allow to free range on fenced in property) ...put them in my compost, and replaced the coop with fresh new shavings.
Now at 3 months they are roosting... So I put a flat piece of wood 3x4 in diameter under their roost, and use a garden tool to scrape & scoop the poop off the board, and into a dust pan. That is whete they do the majority of the mess. If I see any big poops, or stinky evacuation droppings on the shavings I just scoop them up, and toss them into my dust pan for the compost. Then I'll scatter a few handfull of shavings on the floor.
If you're building natural immunities then you want to allow the coop floor to have just a little yuck, but no build up. If it stinks, or smells then you have let it get too dirty, or lack ventilation, and need to change it. I would give it a good sterilization, and airing out after that, but don't let your coop get to that point. It's unhealthy for you & your birds.
For the winter I will be adding a thick layer of straw to the coop floor to help with the cold. Especially since artificial heat has it's drawbacks.