It isn't a mystery at all. The Vita manual clearly labels it as an accessory port. It is intended for connecting Vita hardware accessories, that may or may not be offered later by Sony or licensed third-parties. The PSP had a few accessories, including a camera, and a GPS receiver. They weren't offered in North America, and the Vita has those functions (in the 3G model) already. Other accessory types are certainly possible.
I think that will have use with the PS4 ?
I actually have a big feeling that they had this port in mind way back then to work with next gen hardware. So hopefully we will see something next week for it.