Well, first off, Supergirl didn't have the same ID. Her name was Linda Danvers. Pre Crisis Supergirl was Linda Lee. They actually made reference to the reason for the similarity in the last story arc, where the Supergirl to whome the book belonged to met Pre-Crisis Supergirl in a little time hiccup that landed her in the Pre Crisis DC earth. And, as for her not being Superman's cousin, there was a reason for that. One that I personally agree with. They were trying to have Superman, the last son of Krypton, actually be the last son of Krypton. Not the last son of Krypton, except for those three criminals, his cousin, his dog, and an entire city of tiny people.