yes he does. if you check on youtube, alot of people have uploaded videos of them screaming about his reply. He personalizes them too. :) Kristen also replies to fanmail.
here's a site where people report that he replies.
link
But it does take a while. I'm sure he gets tons of fanmail. And since he's still filming his new movie "Remember Me", he probably hasn't had much time. But from that site, he's still replying! From the looks of it, it takes about 5-6 months for him to reply. But understand he probably gets ALOT of fanmail.
