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For a long time, Navy pilots have been required to be completely free of kidney stones. A few Navy urologists, led by Dr. Masterson, studied this in some detail. They found that in 30 years and 54 million flight hours there has not been a case of a mishap related to kidney stones. Maybe this is because the standard is so high, or maybe it is because kidney stones don’t cause accidents much; hard to say. But a lot of stones are not treated in the overall population, because many can be observed or are too small to worry about. A lot of navy pilots are probably being over treated for simple small stones. Pilots don’t have more stones than everyone else.
If a navy pilot has a stone then a CT is required to prove no stones present and an annual x-ray is needed to make sure it stays that way. The FAA is a little different, requiring only that stones be asymptomatic, not increasing in size/number. One product of the navy requirement is that pilots become reluctant to get a CT, lest they discover and then get forced to treat an asymptomatic, small, non-problem stone.
Hopefully this data will give rise to some changes in Navy pilot requirements. A lot of stones can be safely observed without treatment. A pilot in a multi pilot aircraft crew wouldn’t have to worry as much either. In my clinic a 1-2mm stone would never be treated; there is no reason to prevent a pilot flying with such a stone in my opinion.