Making Missiles is expensive, resource wise. And it is also very inefficient to get to orbit using rockets, on a major colony it might have the economy to support it but why would you when you can just have Orbital Ion Cannons. I think Ground units will not have the range to target ships in orbit, but when they enter atmosphere, they are fair game. Titans with Ion Cannons can blast shuttles and damage Frigates, Juggernauts & Rhinos with AA Laser Cannons can shoot down ships too, Focus Beam can melt through to Frigates, and Skystrike Artillery can be converted to shoot at ships entering in low orbit too. GDI has several options now that I think about it, but other than Skystrike the others are in-atmo weapons not anti-orbital. I think Skystrike is GDI's Stonehenge but lower power and cheaper to make and Excalibur would be a SuperObelisk.
Navy is built from Orbital Shipyards, so no need to launch them from the ground to space. Strikecraft like, Orcas and Firehawks can just got to space with their Stratoboosters I mentioned in their blurb. So no mass drivers.