I have seen newly mated queens lay multiple eggs in cells especially in Nuc’s because of limited egg lay area and they are cranked up in high gear. But you situation seems extreme, also since you couldn’t find the queen in a nuc I would suspect the worst ( laying workers) I have never seen them go crazy in supercedure cells. When workers start laying eggs they can do some crazy things. I like the idea of shaking the hives out, make sure you are far enough away so the laying workers don’t find their way back to the yard and start doing crazy things in a new hive.