I too had a very bad accident as a teenager and had to have my ankle "rebuilt" including a 6" pin and over 20 assorted screws and bolts (kept them in a bag for years to show off at parties!).
A year after the surgery to put them in I was called back to have them removed. As it turned out the bone had actually reformed around 2 of the screws and they were unable to remove them.
I have had them with me for some 20 years now with no significant problems.
I guess the choice is up to your son, if they are not causing him pain and the doctors do not believe they affect future growth or interfere with muscle use then keep them. Otherwise, although it is a nuisance it is so much less painful to have them removed.
Good luck in whatever you decide