I agree with your reasoning, but in practical senses people just don't go anywhere else. I was a pretty regular visitor to Dalimond and Chichonis over the last three months while levelling my STMD, and I made a habit to check the connies there. They all experienced little to no usage. Might be due to the lack of players in that range perhaps, but regardless, no point going to an empty shop!
By removing the connies from those locations, it does in some respect force people to use the remaining Empire-provided ones, or player-built ones. Perhaps with more players joining this may change in the future?