@David: I think the charm was just lucky. It was too thin for something with a primary purpose of protecting the neck. It's actually a miracle that the metal was exactly where it was.

As for it belonging to Subaru, didn't we get some scenes with him after Shun gave the necklace to Saki? That means he wasn't mutated at that point, and I can't see why Shun would take it off Subaru.

Regarding that scene, I had thought the flying balls were marking the physical boundary that Shun wanted to keep from people. I also thought that Shun's reply suggested he gave the only copy of the charm to Saki, who made the assumption that Shun would have given one to Subaru as well.