According to the colorist Nick Filardi, this is really cannon. He made a comment on a Reddit post bringing this fact to the attention of Harry Potter fans to confirm it:
Fun fact: I'm the colorist for that story and originally made him a gryffindor. We went back and forth on a couple rounds of corrections and the editors insisted hufflepuff. That isn't a casual joke. That's deliberate deadpool cannon.
via nickfil