But, we also know that they came up with Photon Torpedoes in the middle of the first season, because they were screwing up with Phasers. It just happened that we never saw a situation in TOS where RCS would come up. There was no drydock scenes, etc. If there was such a scene for TOS, they probably would have been written in ('maneuvering thrusters!')
Unlike all the other aspects of the Trek franchise, TOS was very much a 'work in progress' in nearly every aspect. Nothing was nailed down, and tech and details would change as the show progressed. It's hard for me to be religious in adherence to what we're presented with when I know all of what was going on with the show.
It's not like there weren't OTHER aspects of the Enterprise expressly mentioned that we never see, such as escape pods, aft phasers, broadsides, etc. An RCS system could, for the sake of franchise consistency, just be handled the same way.
But think about what we're really arguing here, a grand total of six clusters mounted four on the hull and two in the nacelles. Really, if it weren't for the big yellow markings for them on the uprated Enterprise, would they be that noticeable?
In this case, I just figure that it's easier to accept that they're THERE, along with the phaser banks, torpedo launcher, and gangway, than invent entire reams of treknobabble to explain why they aren't.