I had my own idea for a Ninja NPC.
Maybe she (let's make it a female ninja to add another female NPC to the game) could be a quest-based NPC like the angler, only she assigns assassination missions where you have to track down and take out unique ninja mini-bosses. The rewards could be ninja-themed weapons for all classes, not just throwing items.
Some ideas:
Kunai: A hardmode consumable upgrade to the Shuriken, that splits into a spread of three kunai.
Windmill Shuriken: A giant shuriken that serves as a boomerang-type weapon.
God Hand: A Golem-tier or endgame upgrade to the Arkhalis/Fetid Baghnakhs, which throws a flurry of rapid punches. ATATATATATATATA!
Nunchaku: A short-ranged flail weapon that hits rapidly.
Flash Bomb: A consumable item that is thrown, and teleports you to the spot where it landed in a puff of smoke.
Blossom Fan: A Leaf Blower-like magic weapon that throws out a cloud of cherry blossom petals.
Shadow Scroll: A summoning weapon. Summons shadowy duplicates of yourself that attack when you do. Gives a 10% chance to evade an oncoming attack by expending a clone.