I have never thought of that before. But I think aliens are smart ?

Not entirely sure, but I'd (unconsciously) do the nod and head shake whether they understand or not. I mean - we didn't even know what could be used to communicate with them so... yeah. Speaking of which, I watched 'Arrival' about a few months ago where the lead role tried to figure out how to talk with them for some purpose, and she did found a way to.