There would still be planetary combat in Freelancer. While there are admittedly few chances for a full scale planetary takeover (with the exception of Kusari -> Harris + Leeds), there are always situations where land forces would be deployed to (or based on) hostile planets, to strike tactical targets or conduct operations across smaller regions, as opposed to conquering the whole planet.
Theoretically, you could have a Libertonian special forces division assault hamburg to destroy say, factories or administrative centres, or have Blood Dragon insurgents entrenched in areas of Kyushu actively resisting the Kusari Army over a long term. Planets are still big places, and it is possible to have opposing factions with planetary combat forces duking it out, on a smaller scale.
Assuming this is such (which I don't see why it wouldn't be) atmospheric combat aircraft would be a nessiscary part of any organised armed force, along with tanks, walkers, armored vehicles, seagoing warships and submarines, etc.
Even if you have spacecraft capable of planetary entry and attack, there's no reason that precludes the development of more specialised vehicles with the sole perpose of aerospace combat. Planetary bases and installations would need something to protect them from low-orbit attacks from whatever, and using stock spacecraft (which are presumably more complicated and expensive then 'simple' atmospheric aircraft) would probably be a waste when you can deploy cheaper, more numerous, and presumably more suited aircraft to do the same thing.
