I believe you are confusing the title of clan '氏' (pronounced shi) with families, which are sometimes also called clans. There was in fact a Hattori family, but they were originally a subservient part of the Matsudaira-shi (松平氏). Throughout Japanese history the most powerful clans were composed of the family from whom the name is derived, and their retainers, servants, lesser samurai etc. They all identified themselves as part of the clan, though they were unrelated by blood (much like how the Yakuza operates today) These retainers themselves may have come from relatively powerful families themselves, but the clans usually had some ancient claim to fame, like nobles in Ancient Rome who claimed to be descended from this god or that goddess (Julius Caesar was 'descended' from Venus). The clan which the Hattori family originally served were reputed to be the descendants of the Genji/Minamoto clan (源氏/源), one of the four most powerful clans from the Heian period. The Minamoto name was bestowed directly upon members of the royal family. This practice originates from the old emperors having too many children and a way to control succession (Those named Minamoto, though related to the Emperor were unable to be in the line of succession). Hattori Hanzou, as both a samurai and a specialized mercenary (aka ninja), would later served the Tokugawa clan as a retainer where he would become famous for saving Tokugawa Ieyasu's life.