Since the comic and the show are no longer in line with the current 52 this is not a surprise.
What??? The animated DC or Marvel shows and the comics based in them have never
been "in line" with the comic continuities. They've always been alternate realities. Young Justice
even made it official -- the behind-the-scenes material asserted that it took place on "Earth-16" within the DC multiverse. So there's absolutely no reason why that would be a factor in the comic's cancellation or the show's dire straits. It never has been before.