The premise of the question may be somewhat off. Elite Kenyan runners do not have higher VO2-Max scores, lactate thresholds, etc than other elite runners. So if the Kenyan diet / training was favoring them particularly, the standard measures of endurance fitness fail to show it. Nor are the other people who train for this kind of thing shy about eating carbs. What has been proven about Kenyan runners is that they are bio-mechanically more efficient (IE their running form is better).

A popular theory for why Kenyan runners are fast is because: 1) They are a culture of runners (much like you expect countries that celebrate soccer to produce the best players). So the best runners are found. 2) A large amount of barefoot running leaves the runners with perfect form.

I'd suspect the long terms affects of the diet are the same for Kenyan runners as they are for anyone else.

I have no information on the long-term health of Kenyan marathong runners.

However it reminded me of an interesting theory for why so many good marathon runners come from Kenya, aparently particularly from the Kalenjin tribe. From here http://www.aafla.org/SportsLibrary/SportsHistorian/1997/sh172d.pdf

Still, while there is something in each of these - altitude, diet, poverty - that helps explain the phenomenon of Kenyan running as a whole, none of them begins to account for the hugely disproportionate success of the Kalenjin. For that, we have to look more closely at circumstances unique to the tribe.

An obvious thought is that the Kalenjin might be endowed with some sort of collective genetic gift. This is touchy stuff, of course, and there is nothing like replicable scientific data to support the idea. But the primafacie case for a genetic explanation makes some sense: the Kalenjin marry mainly among themselves; they have lived for centuries at altitudes of 2,000 meters or more; and, at least by tradition, they spend their days chasing up and down hills after livestock. So it is not unreasonable to suggest that over time some sort of genetic adaptation has taken place that has turned out to be helpful in competitive distance running.

This notion gets some flimsy support from the fact that linguistic data link the Kalenjin to tribes elsewhere in East Africa that have turned out a majority of their countries’ world class runners: these groups, all of them historically pastoral as opposed to agricultural, include the Oromo in Ethiopia, the Iraqw and Barabaig in Tanzania and the Tutsi in Burundi. There is a temptation to imagine a race of lean, cattle-herding uebermenschen wandering up and down the Rift Valley.

What I find more intriguing, however, is the possibility that some of these peoples’ customs might have functioned indirectly as genetic selection mechanisms favoring strong runners. I am thinking specifically of the practice of cattle theft - euphemistically known as cattle raiding. It was common to all these pastoral peoples, but in Kenya, at least, the Kalenjin were it is foremost practitioners. Of course they did not regard it as theft; they were merely repossessing cattle that were theirs by divine right and happened to have fallen into other hands. Never mind that those into whose hands the cattle had fallen often felt the same way. Anyway, Kalenjin raids often called for treks of more than 100 miles to capture livestock and drive them home before their former owners could catch up. The better a young man was at raiding – in large part, a function of his speed and endurance - the more cattle he accumulated. And since cattle were what a prospective husband needed to pay for a bride, the more a young man had, the more wives he could buy, and the more children he was likely to father. It is not hard to imagine that such a reproductive advantage might cause a significant shift in a group’s genetic makeup over the course of a few centuries.

No evidence but it's an fun bit of speculation.

I was reading this today: http://science.nationalgeographic.com/science/health-and-human-body/human-body/unbeatable-body.html.

I don't believe it adequately answers your question, except that I think no studies have been performed on a Kenyan athlete. However, it is postulated that there is a higher than average incidence of osteoporosis. I hope that the osteoporosis diagnosis is not based on a pharma company's aggressive stance on BMI, body fat or bone density readings.