The main reason missile STOs are not in the game is that missiles, unlike beam weapons, require a bunch of extra logistics - magazines, reloading (and how to control interaction with the planetary stockpiles), sensors/MFC resolutions, and so on. How do you control which missiles are loaded, or change the loadout? If you put a passive-targeted missile into a STO, does it need active sensors or a MFC larger than 5t? Current STOs use auto-designed BFCs and sensors, for missile STOs that would not be adequate so you add complication to the interface (which for Steve means a bunch of work to design a useful GUI).
It's not insurmountable but it requires a lot of finicky detail work to get right, so I can understand why Steve doesn't want to do it very urgently. the PDCs in VB6 worked by basically being a special type of ship, which is a design pattern Steve wanted to move away from in C#, so simply reverting to VB6 mechanics is not the solution either.
I also concluded this to be the main reason, but now after reading I really wonder, -if MSTOs are ever to being a thing again-, what would be easier in the end: Having to have a special case of "ship" or having to come up with a whole cumbersome extra munition handling, design and targeting system, which would also just be a special case of the new STOs then.
So maybe launch bases would be something entirely different from the current STOs once more.
--Perhaps a "launch base"/"launch capacity" building? Something that comes from regular factory construction and bestows the colony with launch capacity directly as a colony feature?(eg "Launch Facilities: 220MSP") Then targeting and reload could happen on the colony tab or something where you'd portion your salvo however you like by simply clicking/adding the missiles available you want. I think the sheer size and availability of infrastructure on ground compared to anything spaceborn could easily explain the huge flexibility in portioning and targeting range here, especially if those "Launch Facilities" would be 25kt-125kt+ in size each like all the other buildings.--
Well, though I would in some shape or another find such a system acceptable as a solution, I also kind of like designing facilities myself, so considering that outside of making missile bases their whole own thing there would definitely be a special case (either for ship, or for STO), maybe the process can be made easier by instead having a special case for missiles instead.
If you'd just design specific ground to air missiles whose parameters are known and get locked, then you could make it so MSTOs handle them like STOs handle beam weapons and just purpose built themselves around the weapon they use. So if the missile has 50m range, maybe the base would automatically scale the fire control to match. (not sure how to handle active sensor here though. You'd probably still need a painter in orbit, which is not elegant)
The special case missile I would only argue for so that traditionally more flexible launch bases can perhaps kind of adapt. That is, these missiles could perhaps be part of a series and experience upgrades (eg "Dolphin Punch Mk2") without having to have a new STO.
Just playing some ideas though. I see how range would then still be limited since the STO can't upgrade its controls. Special missiles would only add a benefit for interception and damage I guess, so maybe not enough reason to introduce an exception.
If there would be a "ground force refit" mechanic, which I think is likely to come seeing how cumbersome modernizing and re-organizing ground forces otherwise is, all this need for special cases would vanish, and MSTOs could just be purpose built around the missile they use every time, with only questions for how to handle active sensor and targeting decision making still out as far as I can see.