So if you haven't implemented a ninja class into your database, here's the basic ideas.

High resistance to ice and poison. And/Or high vitality and regenerative capabilities.

They generally have high speed and evasion, and run around in light armor. High accuracy is a must for ranged weapons, like throwing stars and darts. Escape skills.
Rpg maker has a Target Rate parameter; ninjas are associated with stealth, but I would give this trait to their equipment as camouflage.

Head Gear:
Headbands, Masks, Cowls, Visors

Body:
Gi, Shroud, Mesh, or netting (for sound reduction)

Feet:
Tabi, sandals, anklets (increasing movement, jumping, or fall damage reduction)

Weapons:
Shuriken (throwing stars), Blowgun, Tekko-Kagi (Claws, backhand hooks), smoke bombs, Kusarigama (chain sickle), Wakizashi (short one-handed blade)
Steel Wire or Boomerangs are uncommon but not unexpected.

Skills might be called
"Martial Arts" or "Ninjutsu". The use of scrolls is inspired by the Chinese Wuxia and onmyōdō aka yin-yang sorcery.
The most common technique in pop culture is cloning or after-image illusion.
As well as a shadow binding technique, paralysing a person by pinning their shadow with kunai.

You can call kunai "throwing weapons" but they're really more of a multi-tool for cutting and climbing. You tie stuff to kunai, like messages and bombs.