I kept chickens for almost 2 years before I ever felt the need to de-worm them - I didn't see worms or any signs at that time, but some of the hens felt thin to me and they did plump up after the deworming. It took 3 years of owning chickens before any signs of worms in their poop showed up - I just started seeing these white things last Nov. I never planned on giving my chickens medicine and didn't anticipate deworming them when I started, but other pets that spend time outside need to be dewormed - why not chickens too? When we had horses, they were on a strict twice a year deworming plan and we deworm our dogs also. Even if your chickens are kept in a pen, they will still eat bugs, and from what I hear, bugs can carry worm eggs.
I have sand mixed in with the dirt in my run, but I do not keep the chickens enclosed in the run 24/7. I have been using DE in my run, coop, and nestboxes since I first started with chickens - they even have their own sandbox with sand/DE to dustbathe in. They have been drinking apple cider vinegar in their water for about 1 year now.
As for the eggs being healthy - I am sure our eggs are healthier than eggs purchased from cages hens that are not fed natural feed. We do not eat eggs within 2 weeks of deworming and the fact that my hens eat green grass and clover makes their eggs healthier than if they weren't allowed to free-range (the yard is much greener when it's not winter-time). Plus, I can't imagine keep them locked up all day - they absolutely LOVE to run and fly across the yard.
I suspect the wild birds might be the problem in my case. I have tried and tried to keep the sparrows out of the coop/run and have lowered their numbers, but haven't been able to get rid of the sparrows entirely. Even if I kept my hens locked up all day, the birds would still be getting into the pen. If it weren't for the sparrows, the main chicken run would be free of wild birds - the doves, pigeons, and starlings are too big and keep out, but those tiny sparrows are consistent and a problem for many chicken owners in my area.
The run where the feed is kept is made of chain link. Here's the pics to my set-up - both the beginning set-up and the current set-up.
https://www.backyardchickens.com/a/arizonadesertchicks-chicken-coop
After the first sign of birds, we blocked ventilation holes in the coop with wire. We also covered the entire run in chicken wire, hoping to keep them out, but the sparrows fit right through the chicken wire. We then covered the entire run with bird/deer netting, but the birds still find ways to get in - they sneak in between the door and the panels and have also made a few holes in the netting. My husband even built me treadle feeder last year, hoping to discourage the birds, but they have now gotten smart enough to wait for my hens to eat and then they sneak in and dine out of the treadle with my hens.
