I'm planning to seal my roost boards with boiled linseed oil. I read about doing that somewhere. They said sealing the wood helps keep mites at bay because apparently they will take up residence in the boards. The other benefit I see from this would be keeping urine from soaking in. As for the poop, I don't think there is any way around having to scrape them occasionally and since 2 x 4's are not a huge expense, just replace them from time to time when needed.
I would imagine any waterproof type sealer/stain would accomplish the above too, it's just that the site I was looking at said to use boiled linseed oil specifically.