I think it's normal and not to worry about it. I think the clicking is actually tendons , not bones. My own ankle clicks like the devil, since I severely sprained it (on horseback) at the age of 18. It funcitons just fine (at the age of 52).
If your horse is going well, I would not worry. The whole thing with supplements is still up for debate. Some say, when the horse is 14 give supplements no matter the actual performance. But the truth is, the efficacy of suppliments has NEVER been proven. It's all anecdotal and percieved benefit. So if you think it will work, it does.
Things that have been proven to work are hock injections and hylaronic acid, like Legend and Adequan. The Glucosamine/chondriotin stuff is believed to be helpful, but not proven. Sure is a money maker, tho.