A third strike would have been against the fuel farm and the PHNSY. Enterprise still would have been out to sea and Fuchida’s aircraft would have concentrated on those targets.
Due to the smoke from the previous attacks, such targets in harbor may have been obscured, though the ships that left to station outside the harbor would most likely been targeted instead. The Enterprise was less than 200 miles out when the attack started and given Halsey’s aggressiveness he probably would have launched an attack even with one carrier. The Japanese pilots just needed an idea that a U.S. carrier was out there nearby and it would have been sunk. The Lexington was still near Midway more than a thousand miles away and would have been safe.