Auction this thing already! At this rate, completing it in mint condition will never happen.
I am going to say that you a right. Just guessing that the missing cards were inserted in super high end boxes they had at that time. I saw a few get busted with everything not a auto or GU went in the trash. Would bet most of the missing cards are in unopened boxes or in a landfill. What you have now will help people now, the set in a box some place helps no one.