I wouldn't say it's always that clear. Here's two possible scenarios where the context does make the nod a little more obvious in the first than the nod is in second example, but in the first case the guy may be nodding to encourage the guy to continue.
a. Tom said, "Jim, I think you'll Steve is a total idiot to do that!" Jim nods, then Tom continues with ...
b. Dave asked, "Fred, I hear the new guy, Peter is a total idiot. Which one of the three newbies is Peter?" Fred nods, and Dave continues with ...
NB: I don't like this because the nod could be toward Peter or in agreement with the evaluation of Peter. Thus it needs expansion to clarify the meaning of the physical action.
You raise strong objectives, but I'd consider those exceptions, rather than rules, as I'd expect the nod in those cases to be given more weight/explanation, rather than burdening the everyday use of nod with the extra weight every time you use it. That seems to be shifting the burden of the extra context from the rarely used to the commonly used.
As I said, as long as you establish the context of your usage of a term, and then use it consistently, I don't think it's as important to clarify every single use of the term. Readers will understand what you're doing and adapt. In order to ensure they remember, you do need to remind them, so you'd reinforce the 'nod' to accept usage occasionaly, but you hardly need to use it constantly—unless your operating under the principal that you readers are all morons. :(
However, your later example (e) seems needlessly complicated, introducing both the nod and the shrug in the same statement. I'm sure that statement will stop many readers in their tracks, forcing them to reread the sentence several times to figure out which thing Fred is nodding to and which he's shrugging about. Those are two separate actions, and combining them into a single action step seems needlessly confusing.