Ships vs Stations have the advantage of flexibility, scalability and lower individual cost. I am one of the people that build big stations, but I can see situations where I or someone else would prefer ships because they are simply better for the task.
The question is not what is better, but why is it better in situation X. I might have 2.5m ton terraformer station but still use planet based installations for example (if you can spare the infrastructure for population, it is the best).
The ONLY reason why stations might be objectively better is this: No refit needed. None. Zilch. My Sorium harvester station if scaled with enough tanks can seem like a waste but at endgame tech and with a commander it can fill its tanks in two years. In 200 years or whenever, the tech applies to it. Same for terraformer. OR asteroid miner.
Refuelling tech + mining/harvesting/terraforming are techs that do not lead to new component so the biggest problem of bases, that is mostly encountered with Defensive ones (need new guns, sensors, armour etc) is avoided.
On the other hand... they have no armour, few shots and you are a toast. That is why I use mine only with sufficient fleet and JPs protected by bases.