
Nefetiti is a mystery herself. Some think she was Eqyptian from non-royal blood and some theories extend that she came from as far away as the Indus valley. In any case there is no record of any male hiers she bore, Akhenaten and Nefertiti's mummies have never been discovered. Many Eqyptologists (like my step-grandfather who worked in Thebes and Karnak after Carter [see King Tut]) believe a second wife, Kiya, bore him Smenkhare, who was subsequently followed by Tutankhamen.
There are all sorts of controversial theories about Akhenaten: that he was actually a woman or that his protruding belly and breasts were a result of Frohlich's Syndrome. Some actually believe that he was the model for the biblical Moses, or was Moses himself! In anycase Akhenaten was viewed as extremely heretical by the Pantheists who detroyed his new city and as much evidence of his reign as possible after his death. Heck, they could have buried the bodies in the desert, for all we know.
Some food for thought...