Re: John Bonham
I don't hear the shuffle at all on the two live recordings I have (one from How the West Was Won, one from BBC Sessions), but both of those are a little quicker than Zeppelin II and you can definitely hear it there. So, I agree: it could be just an effect they added or it could be the shaker that he had mounted on the top of his hi-hat too. You hear nothing like the shuffle or ghost notes when he moves over to his ride cymbal on the Zeppelin II recording even though the rest of the groove is pretty much the same.
The timbre does sound different to me too - especially immediately after the back beat - maybe that's the shaker and it's a little more prominent there because he's hitting the hi-hat a little harder on the back beat for effect.
Probably not my final answer, but I'm going to say shaker mounted on the hi-hat. Whatever it is, it's a very nice, subtle effect that actually adds quite a nice texture to the groove.
Could it possibly not be a shaker or a studio effect?
I really don't know what time it was. So I asked them if I could stay a while.