I use sand exclusively in the coop. I also have hundreds of chickens. Like you I live in the high desert so any problems with smell or biological vectors is cured by the sun, arid air, and heat. I have made simple a custom rake using 1"x2" furring strips and 1/2" and 1/4" hardware mesh. Imagine the schick shaver with two blades, the first 'blade' or lead being a 24"x 6" 1/2" wire mesh with the second 24"x 6" 1/4" mesh getting the smaller debris. I run this through the coop floor weekly (3/4" of sand). When I do a monthly cleaning I sweep all the coop contents through my sand 'grizzley'. If you've ever seen a construction site with a large metal box with rebar welded in a grid across the top. A loader will dump a scoop on top and the dirt and fines will fall through and the rocks will roll of the sloped grid to the ground. The operator can then use the rocks or the sifted fill dirt as required. The sand grizzley used the same concept. I sweep the entire coop floor contents through my clean-out and re-use the cleaned sand adding a new sand from a nearby stream bed every month. Any moisture or biological is taken care of by the arid air and lack of humidity. The sand in in coop stays a cool 74-78 degrees when the temp outside is 100+ degrees. The poop/straw/sand mix is collected and dumped into one our many developing, raised garden beds for in-place composting with top soil and vermiculite.
I have less particulate matter in the coop generated by bedding ( I use straw in the nest boxes ). So even they get agiitated it's just feather dander and feed dust. I've tried cedar, pine, DE, top-soil ground cover and various combinations of them. The best and easiest to maintain is sand (based on my location, size of operation and homeostasis parameters) in my experimentation. When you are managing a micro commercial flock everything you buy for chickens reduces the capitalization on your product so finding sustainable and free methods is paramount. Hope this helps!
I have less particulate matter in the coop generated by bedding ( I use straw in the nest boxes ). So even they get agiitated it's just feather dander and feed dust. I've tried cedar, pine, DE, top-soil ground cover and various combinations of them. The best and easiest to maintain is sand (based on my location, size of operation and homeostasis parameters) in my experimentation. When you are managing a micro commercial flock everything you buy for chickens reduces the capitalization on your product so finding sustainable and free methods is paramount. Hope this helps!