http://www.npr.org/sections/health-shots/2015/09/02/43674237...
(Audio controls in the left margin.)
He addresses that a fair bit, mentioning that autism is one of the most heritable conditions, and talking a lot about the history of the diagnosis and how it was artificially narrow for a long time.
Personally, my bet is that we'll come to see a lot of autism diagnosis as part of a broader pattern of medicalization of deviance from the norm. And that even the forms we eventually decide are harmful have for nerds the same relationship that sickle-cell anemia does to malaria resistance: a trait that is useful in small doses but can be harmful in large ones.
If there is an actual increase, I'd bet on it being due to stronger assortative mating that has come as mate choice has less to do with geographic factors and more with education and workplace.