Why are you only cleaning "once every month or two"? There's one of the problems right there. Clean it at *least* twice as often as you're doing now and it won't be nearly as bad. If getting the "bedding" is hard or cleaning it more often is too much, then chickens might not have been a good idea. I'm 100% disabled with two crushed discs and every tendon and most muscles torn on the left side of my back. I live on a paltry disability check (darn illegals get more than me!), but I manage to have all the hay I need for the floor and change it, at the *most*, every 5 days.
And yes, if the wood needs to be replaced (I'd replace it, according to the info you've given us), paint it. Paint it on both sides and the edges also. Paint the paneling at least two feet up from the floor.
What are the roosts made of? If they're a plain 2x4, then a flat paint can help. A 'gloss' paint will make it hard for them to grip and slick when they poop on it (think grease on a brass doorknob). It's easier to just replace the roosts if/when they start to get rotten than to paint them.
What are the nests made of? If plywood, then yes, a gloss paint won't hurt them at all and will make them last a heck of a lot longer.