Not only the jewels but a surprising lot of all these valuables: palace inventories, artworks, gold-, silver- and crystalware, archives, collections, etc. have survived the war. The only palace whic was severely damaged in WWII was Huis ten Bosch, since the palace park was used as a site to launch V1 and V2 missiles and therefore it became a target for allied bombers: see Huis ten Bosch in 1951
and Huis ten Bosch now
So it all by all, the jewels, and the rest, survived remarkably well.