I had an older Dales mare on loan, and her joints clicked. She was never lame, and I had her three years with no problems. It did worry me, but her owner said they had always clicked. Did not stop her jumping etc. and like I say she had no problems.
It could be just that your pony is still growing, I have had problems in the past with locking stifles on my native ponies, but they all grew out of it.