I don't think that's exclusively nautical. It was a widespread term derived from a surgeon's tendency to amputate limbs.Dr. McCoy being called "Bones" (TOS) a contraction of the term "Sawbones", which comes from the old nautical term for a doctor... and has nothing to do with a divorce... (ST 2009)
As I kid I thought McCoy was called "Bones" because he was thin.