Hey Will,
Welcome to Permies...
One initial question, just so I can visualize better is this : does the roof of a house with simple cob walls, placed on a stone foundation, have rafters that just sit in the cob, supported thereby? Or is there, or should there be, some kind of top plate of wood or perhaps stone?
First, just to stay consistent, I do not recommend the "novice" ever building structural cob walls. (I know many do, and many are probably just fine) As one of those "alleged professionals" in traditional and natural building, I myself will not build these with out a PE of my choosing being part of the build team. So...infill method...YES...structural cobb...NO! (in most cases.)
Now with my silly disclaimer out of the way...YES, I would recommend there to be a "band beam" of some sort. Most cob builds that support the roof have them or a version there of. Are these in all the designs I have seen around the globe? No. Are they in most (or a form of them)...Yes.
Without a cross sectional schematic and other design blue prints it is hard to recommend what modality to employ.
Also: how do they get those strange wavy roofs I always see on cobb houses. They look like they're framed with wood but I can never see in the pictures I see of them what's underneath. Are they using branches - saplings and stuff?
Give me some links to look at and I can probably tell you the system they are employing...
can a second floor or loft in a cobb house be cob as well, the floor, or should it be wood?
Only if you really have a solid design, and good
experience would I recommend this for any cob structure, let alone a fully structural cob wall system. Yes it can be done. It will take tons of clay and sand, and lots of really hard work...Especially when compared to other vernacular systems.
Again...YES...it can be done...