I think science is very close to determining the cause(s), and I have my own "theories" (quotes because I don't exactly have the kind of credentials to call my own thoughts on possible causes "theories").
In answer to your main question, though, I don't really think that Autism is a condition that's being over-diagnosed the way so many other conditions are. The signs/traits/behaviors in Autism are fairly obvious once a child has reached a certain state of development, and when left undiagnosed and without therapy, only get worse.
People who are trained to detect signs of Autism in babies a year old or somewhat younger know what to look for. The way I see it, if a baby/toddler were diagnosed with Autism incorrectly, it wouldn't be long before he outgrew whatever signs had been mistaken for Autism and began to show signs that he didn't have Autism after all.
Once children get to a certain age, whether or not the have it isn't usually a big mystery to anyone.
I do think there's a time between late in the first year and, maybe, the end of the third year, when parents may be worried that their child has Autism when, in fact, he doesn't. Most parents in that situation would ask for professional guidance/direction on that, though; and I don't think it's difficult for those professionals to sort out which two-year-olds may show signs of Autism and which don't.
ADHD is the one that I think is being over-diagnosed and mis-diagnosed in children to the point that it's criminal.