I think it's a matter of personal preference. I, personally, tend to be more of a "witness stenographer" when taking notes with pen and paper. Because I can type faster than I can write, using a computer allows me more opportunities in class to stop and ponder the material.

I don't think there's any hard and fast rule that says that paper is better than computers or vice versa. Forcing students into using what the professor finds more helpful handicaps students who want to find the method which works best for them.

That study only compared students who doodle to students who daydream in class. They failed to consider that some students actually pay attention and take notes in class -- I think we'd agree that students who pay attention tend to focus better.