Blackberry's have a physical IR port on them, but at this time, because most of the larger customers are very security oriented (or so we think) it is not implemented in the software.
I would imagine RIM has/is/will be working on some different firmware revisions to where people can select the subset of features they want. I think maybe once BES IT policy is mature enough to give administrators a bit more flexibility this all may become a reality.
I think the IR port is for "future considerations" as opposed to wasting this that or the other thing. As BB apps become more prevalent, there may be more of a need for IR printing or such.