In my game, there is a big city (1000+ buildings).
Would it be better to Instantiate every building at runtime (so just the Prefabs would have to be in the game) or can I just place the buildings in the scene?
Does Unity save every object in the scene or just the prefabs and where the buildings are?
I think the question should be : “what is more efficient to do regarding memory and execution time?”
If placing the buildings in the scene is efficient enough? Why bother trying to do something else? But if it is not, try it. There is not a way better than another, there are too many variables to describe something better. You have to address it considering your project.
Try the solution you are the closest to and then if it is not efficient enough, try another one on a different version control branch or with a backup of the original solution. The comparison is key here.