What are those punched out holes in the passport or does nobody know at this point? I did find it weird how the bodies were pretty much all in tact and the passports that were being shown around looked pristine. I'm not saying there's a conspiracy there but it was surprising to me.
That kind of stuff happens with in flight breakups. There were quite a few intact bodies with TWA 800 as well. Depending on angle and speed of descent etc. this kind of thing is not unusual.

the size of the holes in invalidated passports is defined by government regulations. All Dutch consulates worldwide were required to purchase expensive hole-in-passport-makers issued by the Dutch government; commercial products dont make the right type of holes.
My comment was more toward the corpses than the passports.
I would imagine though that it isn't unusual for boxes of invalidated passports to be part of the cargo on international flights. Passenger jets carry cargo all the time and in certain instances invalid passports are returned to the issuing government.