I kinda avoided counting down the total number of ships destroyed specifically to discourage people from doing things the hard way.
There is an event that checks to see if a ship has been destroyed. If it was scanned and revealed to have valuables, a variable is incremented by 1. If it was destroyed before being scanned or was scanned and had nothing of value, the variable is not incremented. Blow something up that satisfies that second conditional and the variable will not be incremented. If you don't scan anything ever, the variable will always
== 0, regardless of what gets blown up. Every time the variable is incremented +1, through some annoying FRED-fu, the directive counter will increment -1. The directive counter starts at 5. For example: variable == 2, directive counter on screen == 3. I can assure you quite confidently it's not a bug.
I know it's hard going if scans aren't made prior to the fireworks starting; maybe I should have emphasized that in-game more. I can't remember if scanning things is in the directives or if scanning stuff is mentioned outside of the briefing but I'll check when I get the chance.
You might be asking why I used a variable for this when a non-variable approach would be much easier. Well, the problem is the cargo is randomized every time you play the mission. Hence I can't actually tell you which ships to destroy because I honestly don't know.
If you're really curious about the mission mechanics you can crack it open in FRED2. Even I can't do that right now. *grumbles*