Got any pictures? That would be helpful in answering your question, and also this sounds like the type of frame I would like to see since German frames are something of my specialty.
At this description, those sound an awful lot like the types of notches that would be made if one were to wattle and daub a building, but the fact that they are only on the undersides of these members seems to suggest otherwise.
It is entirely possible that an original infill may have been removed and then replaced by siding, and it is also possible that an originally intended infill may never have been done, and sided instead.
