Why not? He’s already fulfilled his role in the story, and Shanks actually killing Kid and crew would actually be positive character development for Shanks and prove that Oda was right when he said that Shanks is scary if you harm his nakama.
There’s also the fact that, if Kid is alive, he’d kinda have to resurface on Elbaf since he sank right off the coast of Elbaf and there’s no other nearby islands for him to wash ashore on.