Personally, I suspect it's because launching missiles out of the bottom of a gravity well is just...kinda troublesome.
Still would be fun as an option, but I think it would need purpose-built railguns just to get the missiles into orbit. So basically something that took a lot of effort to build, but was relatively cheap. And also completely impossible to move, since you can't 'transport' 50 miles of underground accelerator.
It actually would be a really cool thing if they weren't STOs or ground forces, but rather literally an installation that was not possible to transport. Would make some planets VERY difficult to attack, but require quite a lot of work to make that happen.