As a follow-up I did some quick research on the internet and found the following article. I don’t know who this guy is, but this article makes a lot more sense to me than the “Okinawan-Peasents-Used-Nunchaku-To-Fight-Samurai-Story”.
http://members.tripod.com/~Nunchaku/about_e.htm
The real history of the nunchaku
Part One
In a popular myth which has been repeated in book after book, we have been told that the nunchaku was originally a rice flail which was converted by Japanese farmers into a deadly weapon to fight against samurai. This myth, however, is incorrect on all four points: The nunchaku was not a Japanese weapon, it was never used as a rice flail, it was not developed by villagers and it was never used against samurai.
The nunchaku, as we know it, comes from Okinawa (Uchina), today a part of Japan. Okinawa lies almost midway between Taiwan and the Japanese “mainland”, and is the largest island in the Ryukyu (literally “rope”) archipelago, a 650 mile long chain of small islands between southern Japan and Taiwan.
Okinawa today is part of Japan, but the Okinawans are not Japanese and have their own culture and language, although the latter is gradually being replaced by Japanese. The Japanese language does not even contain a word for the nunchaku. When one needs to write “nunchaku” in Japanese he may do it in one of two ways: He may use katakana, the syllabic/phonetic alphabet used in the Japanese language to write foreign and loan words, writing the syllables “nu-n-cha-ku”. Or, instead, he may use the Chinese characters for “two member stick” (or “double part baton”), which is pronounced “shuang jie gun” in Chinese, “nun cha kun” in Okinawan and “so setsu kon” in Japanese.
Many think that the nunchaku has descended from the rice flail (utzu), but this is erroneous. To understand why, imagine that you want to use the nunchaku to thresh rice stalks laying on the ground. In order for the swinging arm of the nunchaku to land flatly, you would have to bend over with your head close to your knees or kneel on the ground. In the former position, every time you swing up the flailing arm you might be struck on your back, while the latter position is not really functional as anyone who has had to kneel on rice can tell you. The actual Okinawan flail, like the European flail, has a handle as long as a man’s height to make the threshing process easier. So the belief that the nunchaku descends from the Okinawan rice flail is definitely baseless. Another reason for this error, besides the obvious resemblance of the flail to the nunchaku, may be the existence of the a combat flail (uchibo), which really is a modified rice flail, among the weapons of Okinawan kobujutsu.