Put me down as one of the ones that was blown away by the reveal. And I agree that Phineas is too young to be Ari's son. I'm trying to recall, didn't Sahar/Sarah mention something about a custody battle with her (presumed) ex? And I think Phineas mentioned something about staying with his father. So apparently at some time, Sarah/Sahar was with a amn who was not Ari and had a son (I doubt that a kid of Phineas' age could carry off a story about that, i.e., S/S was doing a long game, but he wasn't). So I suspect S/S came to the US at some point to start the long game to get Ziva (who was working with NCIS at this point), and along the way met a man (either by design or not) and had Phineas (again, either by design or not).
I feel bad for Gibbs, knowning that he is going to have to tell Phineas something that will shatter him. For all of S/S murderous intentions toward Ziva, she seemed at least to be a loving, if strict Mom. It will be interesting to see how this plays out. If the father really exists, he now would have sole custody, obviously Phineas is too young to be emacipated (sp?) if he really doesn't want to live with his father. Should be interesting.