see "Neato Construction Revisions 2011" http://www.robotreviews.com/chat/viewtopic.php?f=20&t=15940
The computer can be programmed to use the connectors in different ways as revisions are made to what connects to it. Each of the connectors has a sort of general purpose quality. There's a kind of leap frog where the wheels or something can be redesigned and eliminating one connection, then the system board gets revised later to eliminate the unused socket. The newest main boards are different than the old XV-11's and cannot be used in those systems. They even require a different software program to use their different connectors. Vic mentioned once that particular connector empty on the XV-11 was originally for a motor temperature sensor line I think, and they combined it with something else or whatever. The original system had an internal connector for an RS-232 serial communications port pararelling the USB, but that is now gone or at least changed to a board edge connector instead of a socket. See Vic7767 posts for pics.
Caution that empty socket is easily confused with the Lidar plug the same size, when assembling.
There's a bit of illusion in these little low power devices appearing to require simpler parts than a big machine like a car, but it's interesting they get quite complex with temperature sensors and the like, putting so much power releative to the size.