A lot of ninja weapons were originally farm and kitchen tools. Nunchuks were originally based on a tool used to grind rice into flour, spades used to break up soil became hand held axes, even water jugs became a special type of boots that can in the right hands be used to walk across small bodies of water
Nunchucks were not used by the ninja as they are a traditional Okinawan weapon and like other traditional Okinawan weapons and martial arts, such as the tonfa and karatedo, they were not introduced and popularized in the rest of Japan until the late 19th/early 20th century.
Also, since we're talking about ninjas, they were only referred to as such in the 20th century, historical ninja were called shinobi-no-mono or just shinobi. Ninja is just the classical Chinese reading of the characters for shinobi, and the art itself was called shinobijutsu.
Anyway, after the establishment of the Koga and Iga schools of ninjutsu, there became a clear distinction of two types of shinobi.
The first type who are much narrower in scope were samurai who were formally trained in Koga and Iga, they acted as mercenaries selling their services to any daimyo who required them.
The second type, who were much broader in scope, were any samurai, bandits or peasants who were partially trained in ninjutsu and led by an actual ninjutsu master from Iga or Koga as his assistants, as well as any samurai, bandit or peasant without formal training who were nonetheless hired to perform one or more jobs associated with the ninja as they possessed those particular skills. For example, one of the famous ninjas of the era, Fuma Kotaro, was most likely not a ninja in the narrow sense of the word, and records indicate that the Fuma were either bandits employed by the Hojo clan or a retainer family under the Hojo clan which specialized in guerilla warfare.
The only famous ninja of the era who was most likely actually formally trained in ninjutsu was Tokugawa Ieyasu's famous retainer Hattori Hanzo Masashige, also known as Hanzo the Demon.
Fuma Kotaro as mentioned earlier was not formally trained in ninjutsu, Ishikawa Goemon was just an outlaw, there is very little known from historical texts about Kato Danzo and nothing about all of the feats of ninjutsu he supposedly performed, Mochizuki Chiyome most likely never existed and the Ten Braves of Sanada were invented in a folktale.