A local journal from Honolulu, the Star-Bulletin, states that this famous gesture comes from a worker that used to harvest sugar and lost his three middle fingers working on his farm. From then onwards Kalili Hamana from Laie started to look for the sugar cars and when they were completely empty he started doing this signal.
A second story says that the Shaka sign came from a mug game that everyone had to do. Another story claim the word came from "shark eye" and when surfers did this gesture, it represented the head of the hammer shark, a respected animal in the Hawaiian culture.
There are loads of others theories about the shaka sign; one says that the Spanish Immigrants in Hawaii started it as a friendly gesture to share drinks with the local people. Another one is that one king in Hawaii, 900 thousand years before Christ, who loved to surf, lost his three middle fingers of one hand in a shark attack. So to compliment others surfers in the water the king used to show the hand without fingers, and before long on it caught on.
It is possible that the origin of the sign is really unknown, but it is always good to do it while surfing to compliment others surfers and create a relaxed and friendly environment in the water. Just don't forget some other important etiquette too!