Officially, Ninja Spawn's first appearance is in Spawn #297, in a panel showcasing a bunch of popular
action figures alternate Spawns:
It's nice, but he'd already appeared more than a dozen years earlier. 2006's Spawn #160 saw Al Simmons fighting a divine enemy in the Garden of Eden. With literally no explanation, two other Hellspawns showed up to help him fight:
Initially they were just lurking in the trees, but eventually they got into the action:
And that is unmistakably Ninja Spawn, almost exactly as he appeared in Spawn Series 29 (released the same year as the comic):
(For the record, here's what the 95 figure looked like:)
Now, what's really of interest to us in that comic art is the other Spawn who's there. He's never out of shadow, but the armor on the shoulders and the crest on his head definitely have a samurai armor feel to them, don't they? What do you think the odds are McToys was working on a "Samurai Spawn 2" figure to go along with Ninja Spawn 2, and this was meant to be him? There's even this piece of Philip Tan art that was used to solicit Spawn #158, showing more of what the design may have looked like:
We can't say for certain that's what happened, but it really feels like McFarlane cancelled the toy for some reason (possibly [hopefully] because they realized it looked like crap compared to the real thing), and while it was too late to take him out of the comic entirely, they could definitely just ink over him and leave him a mystery.