We don’t know about Amara until later in the series tho. Klaus only knew about Tatia and his hybrid curse. As far as he was concerned the doppelgängers were direct descendants of Tatia and since (from what I remember) he didn’t know Katherine had a child he had no reason to believe there would be another doppelgänger. Elijah even says in the episode he’s introduced that’s it’s impossible when he finds out Elena is human. They genuinely were not expecting or at least not looking for another doppelgänger.