Interesting enough is where did the Hornet or Intruder come from that was actually armed? Launch the Alert?
During my timeframe, which I believe encompasses the shootdown, I never flew without ordnance off the carrier unless it was CQ or a fly-off. Even in peacetime, the ordies always loaded one of everything (air-to-air) for captive carry program that rotated missiles out of the magazines and checked their status. In 1993 however, several blue-on-blues changed that and the rush was on to provide CATMs. I know Hornets fly better with Sidewinders on the wingtips anyway.