Generally, it's because the eyes are important for expressiveness, but unnatural anime hair with massive bangs would cover up too many characters' oversized super-expressive eyes. Additionally, cheap animators often draw the hair first and then the eyes, and due to massive laziness and the limitations of paper, they just draw the eyes on top of the hair.
Well, that's how it STARTED, anyway. I'm fairly sure most of the above hasn't been true for many years. For whatever reason, I'm pretty sure they do it on purpose now - pic related, as Signum's hair-behind-eyes syndrome has always been particularly noticable, and if it were accidental they'd have fixed it in the DVD version since they reanimate a quarter of the show for the DVDs anyway.