To be clear, I don't believe we ever did use pens in work stations. As far as I know, we've always used pencils.
The benefit of pencils, beyond the fact that they are economical, is that they don't dry up, and they don't smudge. If you start using ballpoint pens, for example, and you store them for four years and the leftovers stay on.... Some pencils have been in our box for several cycles. They always work. If you buy pens, you have to verify that they work. Even if they do work, sometimes they may smudge, and that could cause ballots to be rejected.
Our preference is for pencils, but we do not disallow the use of pens.