okay hear me out: "nice" is not an intrinsically hufflepuff trait. the intrinsic hufflepuff traits are "loyalty" and "hardworking".
JD is loyal to the point of it being a problem (he's willing to kill tons of people for Veronica)
he's also hardworking, as seen in his complex plan to destroy the school.
also JD's "color" is black and hufflepuff colors are yellow and black.
conclusion: JD is a hufflepuff.