Though not a primary weapon of the Ninja, nunchakus (also known as "nunchucks") were used because they could be adapted for many situations. Aside from being easy to carry, the nunchakus were used to defend against most any weapon from a bo to a sword. By trapping the blade of a sword with the chain between the two sticks, a Ninja could entangle and disarm a sword-weilding attacker.
The same concept applies to almost every other weapon. The nunchakus were not just used for defense, they could also be effectively employed against an enemy in an offensive way. The Ninja could strangle an opponent or even execute joint locks with the chain or cord between the two sticks.