Some of the gymless towns were given Pokemon Contests, so four of them (Slateport, Verdanturf, Fallabor and Lilycove) will be visited sometimes. Plus, because of the Pokemon Contest I believe that they'll be visited even more than the gym towns. They got a bit forgotten in Emerald Version, because all the contests were moved to Lilycove, so Lilycove became overvisited (not only because it includes all the contest ranks, but also because of the department store).
Besides the Pokemon Contest, any gymless town has its own singularity and there isn't any problem if you will not visit that town again to make any thing inside it. The simple fact you need to fly to that town to rematch a trainer at a route in its side is already enough to make that town an important point.