Yae's alternate costume is based off the character Lum Invader from the anime Urusei Yatsura.
Inside Kenzo's house in Edo, where you need to get the chain pipe, there's a poster for Goetanic, a parody of director James Cameron's film Titanic.
In PAL regions, the game was released as Mystical Ninja 2 Starring Goemon, to serve as a follow-up to Mystical Ninja Starring Goemon, despite both featuring different style of gameplay.