As far as I can see I'm not sure the pilots knew exactly what they had on board. The manifest from New York to Ams (now available and readable in the press here)) mention explosives, ammunitions (cartridges) F-16 spare parts and missiles, as well as a number of poisonous gases apparently the engredients necessary to make nerve agents.
The men-in-white -overalls and O2 masks that appeared just after the crash and were picking up debris have now ( again according to the media) been identified as military Bacteriologic and Chemical experts belonging to the Dutch Ministary of Defence.The actual Prime Minister of Holland is reportely very mad at this because he ( again apparently) he was never told. the parlementary inquiry is attempting now to find out who knew what and when..
For memo the then Ministary of transport reported to the media that the aircraft only carried Flowers, Perfumes and videorecorders...
As to the reason of the crash, it is not directly the physical loss of 2 engines on the same side ( not apparently known by pilots )but the rupture of some hydraulic lines on that wing.Initially the aircraft was flyable and therefore could return to AMS .
As soon as they lowered the flaps, which on the 747 are linked to slats deployment, they had assymetric slats deployment , and combined with the lack of thrust on that wing . it rolled and inverted the aircraft, they could not maintain altitude and crashed.
This is at least what the accident report says in a nutshell.