Many horse owners like me deworm their horses every other month by rotating though Pyrantal Pamoate, Benzimidazole and Ivermetcin twice each year. They are meant to kill most of the worms within a day or so of treatment. The worm population begins to recover quickly so the next round of treatment is needed before the worm population gets out of hand. Penn State says that the average 1000# horse produces 50# of manure a day, so the wormer would probably be measurable for only a day or so.
Some horse owners use a daily wormer or daily feed through fly control. The feed through fly control is meant to pass through the horse's gut and interfere with the growth cycle of flies. Either of these could possibly interfere with soil biology.
But if the manure balls and bedding breakdown over time into compost, some types of soil organisms are surviving. I have spread the composted manure of my 3 horses on my gardens for the 5 years I have had them, each year I get better results. In fact I picked up almost 2 full-sized pick up loads from a neighbor to expand my gardens and I expect great results.