I'm a big X-Phile but I honestly never picked up on that. These mannerisms make sense in regards to his character's history: through flashbacks and anecdotes, he was apparently a normal kid with normal interests (baseball, TV, etc.) until the trauma he endured by his sister's abduction, which fueled his lifelong obsession with the paranormal and finding out what happened to her. He was ostracized by his peers for his interests (hence the nickname "Spooky", for his beliefs in the supernatural) and even by his superiors, so of course he would become pretty much isolated; the Gunmen are the only (somewhat rational) people who believe his theories and Scully was merely assigned to him whether she liked it or not.
Outside of his work, he's presented as a pretty normal guy, even so much as a stereotypical American male who drinks beer and watches sports games on TV. He's shown sympathy and empathy towards a lot of victims and he most notably has a strong sense of humor and cracks a lot of jokes. Also, as far as "very little facial expression and body language", well...David Duchovny's not exactly the most dynamic of actors.
I can see how someone could come to that conclusion, but I think under closer scrutiny, it just doesn't hold up, at least in my humble opinion.
Though there are degrees of Aspie-isms, where some have autistic traits more so than others.