She's Japanese-American, emphasis on the American (i.e., born and raised and, as a result, is only familiar with American culture).
Many people have pointed out that, on the topic on her ignorance of anime, her being of Japanese descent is less relevant than the fact that she's a student in computer science, and therefore has had supposedly much exposition to nerd culture, of which anime is a significant part.
But from what we could see of her since she was introduced, obviously, standard categorizations don't work with Emily.
EDIT: This is pure conjecture, of course, since we still know very little about Emily.
Well, for one thing, with such a first name, it's unlikely she's Japan-born. Unless her parents are at least half as excentric as she is, which can't be ruled out.
At times, I wonder if Emily is not a catalogue of quirks Jeph couldn't include in Hanners character without breaking it (and its tragic aspects). She bears a tidbit of similarity to Hannelore as she was when she was first introduced.
By the way, I'm a programmer. I briefly tried to imagine what code written by Emily would look like. I gave up.