"Bones" is short for "sawbones", which was a widely used slang for doctor during the 19th century. But the evident reason that a 19th century word shows up in the sci-fi Star Trek is that the writer was trying to create a naval atmosphere and the word was originally the traditional name for ship's doctor in the British Royal Navy. In those days the chief duty of a ship's doctor was performing amputations. This naval usage predates the more general one and was continued longer. Many of the parts of the Star Trek spaceship are named as they would have been in old navy sea going ships. The ship is run from "the bridge" for instance, not from "the cockpit" as if it were a plane. The ranks and positions of the crew are also naval, as are customs such as the captain calling the officers "Mr.". So, the spaceship doctor is called "Bones" because he is the ship's doctor. No one would have given him the nickname, it is just part of naval tradition carried on into space.
Source(s):
http://forum6.wordreference.com/showthread.php?t=1028518
http://encyclopedia2.thefreedictionary.com/sawbones


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