It's probably because in conventions where there are a limited number of tickets available, homestuck cosplay is generally very low-rent and means fewer types of other series cosplay, or something.
It makes some sense for anime conventions to frown at homestuck cosplay, but I don't really see the point in banning it from comic conventions (given that it is, in fact, a comic). Granted, such a ban is likely impossible to enforce anyway, outside of preventing "official" meetups like the ten million people who applied and were rejected for a Homestuck panel at Otakon last year.