Director's cut
In the collector's DVD, interviews with the staff and writers concede that Ninja Ninja is indeed imaginary. However, even though Ninja Ninja is "imaginary," he appears to have some form of presence in the real world, as well. When Brother 2 of the Empty Seven spies on Afro, Ninja Ninja can be clearly seen from Brother 2's point of view through the binoculars. Ninja Ninja also interacts with items around him constantly such as catching Afro's spliff in his mouth, moving a hanging pillar inside Otsuru's home, putting Otsuru's comb into Afro's hair, eating the food that was intended for Afro given by Brother 3 (as seen in the Director's cut) and throwing the Afro-Droid's microchip at Afro to cut in two. The idea of Ninja Ninja having at least a partial existence, in reality, is once again brought into light when he is 'killed' by Kuma. Because Kuma was such a skilled warrior and had the intent to cut down Afro on the sword strike that killed Ninja Ninja, it would seem odd that he would pause from his attack and have a conversation with Afro if there was not a reason to give pause which strengthens the idea that he was taken aback by Ninja Ninja's sacrifice before attacking Afro again. Additionally supporting his real-world presence is the scene in the video game in which he knocks the hand of one of the Empty Seven off of a ledge, killing him, as is the scene after Sword Master's death in which one of the many clones of Ninja Ninja grabs Sword Master's mouth and moves it up in down, pretending he is a puppet.