Is Ninja a type of magic, and why does my father object to it and recommend Karate, and what is the truth behind the Ninja's supernatural abilities?

It is advised to be dutiful to one's father and obey him, as long as he does not command disobedience. Karate is permissible under certain conditions. As for Ninja, its true nature must be investigated; if it is proven to involve sorcery, then it is impermissible due to the danger of sorcery and because it is disbelief (kufr). One must obey the father if he forbids something permissible.