Should they be limited to the relating parts of objects? Should they be all of the structures? The entire games textures? At what point is a atlas more costly than helpful in this type of game?
I’m assuming you want to keep them somewhat apart to be able to unload unused parts.
The absolute max size will be limited by the device you are deploying to (e.g. earlier versions of mobile devices).
What is best for you is not necessarily the same as for everyone else. I would suggest determining the smallest texture sizes you are happy with for all your individual objects, and then sensibly combining the relevant ones into an atlas (i.e. if you have a number of scenes with only a few of the textures being used then you may not want to load the entire atlas - so try keeping those separate). Once you have done this deploy it to your intended device and simply try it out.