This seems to be this recent opinion that you need to do something to your plywood flooring. You don't.
Since your flooring is going to be covered by several inches of shavings or straw, wet poop never reaches the wood. It eventually dries, and may later make contact with the wood, which will do no harm.
Let's pick a really worst case scenario: let's say the floor gets tons of water on it, and tons of wet poop stuck to it. Let's further say that the wood is damaged beyond repair. Even in this very unlikely event, a portion of plywood may be cut out and replaced!