I am pretty sure you can't build big ships on a planet, you would have to do that in orbit, since they are not built to launch from the ground.
And if we are arguing that you do not have enough supplies to blow up stuff on the planet, where would we get enough soldiers to actually occupy one? I would think that that needs at least a few million soldiers. Though i have no sources for that, i would guess that you need at least similar amounts of space to transport enough soldiers, food, and equipment to occupy a planet than you would need to just blow that area up.
But i agree, you would probably need specific equipment to blow up stuff on planets, most of your ammunition surely can't pass through the atmosphere easily. But you would also need soldiers and more to occupy a planet and take what you want, so unless you plan a longterm occupation, just bringing some anti-planet weaponry with you and saying that you will blow up a city each hour until they give you what you want is probably far more cost-effective then bringing loads of soldiers and fighting a ground combat to gain that. You don't even need that much stuff, just load a freighter full of nukes, or whatever future weaponry does that thing more effective, and you are done.
And occupying a whole planet for a long time would use up an incredible amount of resources. Just look at how many soldiers and money are needed to occupy for example Iraq or Afghanistan, and then extrapolate that for a whole planet.