How to include submodel into main model in LeoCAD?
I have now figured out that you can include submodels the same way as normal parts. In LeoCAD, go to the parts panel where you can select a category ("All Parts", "Parts in Use", ...), scroll to the very bottom and select "Models". Then you can select your submodels and incorporate them.

(For some reason, my submodels still don't show properly in LPub3D, but I guess that is a separate question.)