In my playthrough, he disappeared after giving me the "All in the Family" quest, too. After a while I gave up trying to find him, but eventually realized he was on the ship, sometime in the next arc. Not sure how long he had been there.
But that was a long time ago, before all the fixes that were supposed to fix all the issues with him going AWOL. Either way, his quest is not essential. Just keep playing and maybe he'll show up on the ship eventually.
