It does make more sense if you consider that it is part of a line of Hedgehog genes, all of which make Fruit fly embryos look like hedgehogs (spiky) if they’re inactivated.

They didn’t just go “Let’s name a gene with bad outcomes if mutant in humans after a video game character! Yipee! Hooray!”, at least not for that.

Though they did name SHH’s inhibitor Robotnikin.