If it is a raw wood floor, not painted, then that floor has absorbed everything.
I'd clean it, hose it, clean it with ammonia and dish soap, rinse, let dry, air out and then put several coats of exterior latex paint.
That will help it from absorbing more stink.
If they have water in the shed, you need to devise a way to not have that water all over the place as that will just soak into the wood.
Sweet pdz (I think) is used w horses and helps control odor. Might work mixed in/under their bedding. I've used it w chicks, but not ducks, so check it is safe if they snack on it before using.