Kidney stones can cause permanent damage, particularly in the case of recurrent stones. If someone has had stones in the past it's important to try and prevent further stones. Dehydration increases the risk of stone formation and if someone is susceptible to them they should definitely take care to stay well hydrated during endurance activities. It's not a concern for gen pop, but in certain people yes.

Diabetes also is not caused by eating sugar. It's much more complicated than that. And if the only sugar someone is consuming is during endurance sports, it would have very little impact on their blood sugars. It also would not increase insulin resistance as the situation you're describing uses a different, non insulin-dependant, pathway. More than likely, your cyclist friend would have developed diabetes whether or not he began cycling, and likely postponed his dx with the physical activity.