Not only is she smiling, but it's official art. Well, then again Nagato once has an emotion overload and steal's Haruhi's powers, rewriting the world where no one has any special powers. She's then just a normal, if overly timid, high school girl with a crush on Kyon and, yes, she smiles at him a few times.
I'm guessing Takari only watched the anime. Heck I didn't read a page of the manga (cant find scans and dont wanna order the real thing just to be stuck not understanding the language.) and I know she smiles at least one tine cause of personality change in an alternate reality thingy... man I really need to get a hold of the manga at some point.
The Yuki that smiled was not this Yuki. No glasses and a Yukata with Goldfish puts this at Endless Eight, and Yuki had NO reason to smile during that fiasco.