Some software can easily extract midsurfaces in most cases (apart from really complex ones). Offsets are not very intuitive (or even counterintuitive) and you have to be aware of the normals. But it’s up to the OP, of course. Above, I presented both approaches.
Shell thickening is always an option. It wouldn’t be needed e.g. in Abaqus, but CalculiX has multiple issues with shell elements, including what I’ve mentioned about rigid body constraints. So thickening at least some parts can help (otherwise, you may be forced to run linear calculations for now): Known CalculiX limitations
Submodeling is definitely helpful for large welded assemblies since you can refine the mesh in the weld region or even change the way it’s modeled or its geometry. Shell-to-solid submodeling is natually usable in CalculiX (thanks to internal expansion to solids) as well.