Well-made swords possess great value as heirlooms and inheritances in many cultures, the japanese being one of the most notable. Reasons for their conservation may be as symbols of birthright, ancient oaths, power, ancestral victories, religion, blessings or curses.
In modern media relating to ninja, it's common to see ancestral weapons (often swords) used as plot devices. One reason for this, besides representing old lineages, may be reference to Fudo Myo-o, a Buddhist dharmapala considered a patron deity of ninja traditions and represented holding a flaming sword in his right hand.
In Shinobido Edit
One was originally used by an ascetic, the ancestor of the Asuka Ninja, to fight Gamuran and later seal his soul inside the blade, which was then guarded inside a small shrine; presumably the sword is or became supernatural in nature, thus why it's capable of harming the fully revived Gamuran. It was ultimately used by Goh to finally kill the evil priest.
Since the end of the first game the sword has not made further appearances. Either it's still in the surviving Asuka's possession, or was destroyed along with the shrine.