I do this - in fact most of my joints click, many involuntarily. It's mostly a bad habit, but it may mean your DS is slightly hypermobile which could be worth getting checked out. There's no evidence it leads to arthritis but I understand that it sounds a bit gross to everyone else. It may be worth getting his feet checked to see if he has any tendency to under/over pronation, in which case he could be given some strengthening exercises and possibly orthotic inserts.
I wouldn't worry. Oh and I'm not in any way a medical expert; I just have a similar habit.