If a kitten dies after birth then it should be handled as any pet death is handled, by finding a way to properly bury or cremate the body. It can be devastating to lose such a young life, but it is important to keep the body cool in the refrigerator or freezer before burial to avoid odor and deterioration.
If the owner or breeder wants to know why the infant kitten has died, then the body should not be put in the freezer and should be taken to a veterinarian as soon as possible for the necropsy. From here, it must be decided how to pay the final respects and where the body's final resting place will be. These are all individual choices and should be left up to the kitten's owner.