He did show traits like arachnodactyly, an unusually long face, a tall, slender build, and a wide pelvis. His relatives are shown as having similar features, and elongated skulls. The fact that the rest of his family apparently showed some of these traits also suggests that he had a genetic disorder such as Marfan's Syndrome. He also lived for about the amount of time that a Marfan's victim lives without medical assistance. There is certainly a possibility that there was nothing wrong with him.
Any conclusions drawn simply from looking at artwork are highly questionable.
If historians three thousand years in the future were to come to the same sorts of conclusions from looking at today's political cartoons, for instance, they would probably think that just about every president or political leader that the U.S. has ever had suffered from some kind of bizarre disorder. A good many people have offered alternative explanations as to why Akhenaten was portrayed so strangely. One theory is that it was some form of religious symbolism. It has also been suggested that the distinctive art of this time was some kind of expressionistic art style, and it has been pointed out that everyone depicted in the artwork of the period showed some of the odd features of the king and his family. One thing that would suggest that Akhenaten did have an illness of some kind was the fact that he remained hidden for a good portion of his father's reign.