Why should AKE LD3s not be used in the A380?
Emirates uses multiple kinds of ULDs.

The AKE with "DO NOT USE WITH A380" are made out of aluminum metal. The tare weight is 80 kg. Contrasted with the AKE (light weight) 66 kg tare weight and the AKL (ultra light weight) 56 kg tare weight, the difference may seem small, but multiplied over the large number of AKEs can reduce the payload and therefore fuel burn considerably. 

Emirates Skycargo website.