...putting scratch on top of the bedding to encourage them to dig doesn’t increase illness? Eating on top of poop piles?
Not that I am aware of. The scratching and pecking for food inside the coop helps to move the chicken poo to lower layers of the deep bedding.
There are entire chicken raising systems that put chickens out to pasture after the cows have moved off that grass. The idea is that the chickens will tear apart the cow pies and find good bugs and worms to eat. So, they help to spread the manure fertilizer as they are rewarded with good stuff to eat. Nature has a way to maintain balance.
Digging in dirt to get grub is what they do, so digging in bedding is normal behavior, good for them.
Having fecal samples run at your veterinarian's is good practice, done occasionally. Birds at some properties will have few intestinal parasites, while others will need worming often.
Mary
@Folly's place I have never noticed any worms in our eggs. Do you send in samples to the veterinarian's lab if you don't see any worms in your eggs? How much does that cost? Or, do you just periodically add some dewormer to the feed?