Last year I read a novel where someone furrowed their brow about once every two pages. Not just someone, but everyone. All the characters did this. It drove me crazy.
Sure, brow furrowing is a common thing to do when you're puzzled, but I think distinct characters are more interesting. If one furrows their brows a lot, perhaps the others (at least some of the others) should express this metal state differently--a head tilt, an exclamation of disbelief. And there's no sense of degree. A furrowed brow should express more confusion and surprise than a "huh?" and perhaps less than a gaping jaw.
What worries me about smiles and nods, in particular, is that those are indications of agreement, which is the opposite of drama. Drama is conflict. One of the best pieces of advice I ever got was to make your characters argue. Sure, your main character has a certain mindset that suits the story you've envisioned. But you can surround them with foils that have a different point of view and thus react differently.
As Secespitus wrote, context matters. If the main character is smiling and nodding to mask their true feelings, then make sure the reader knows that right there at that moment. The conflict between the feelings and the action is a tiny bit of drama. No thesaurus needed there. If I had too many smiles and nods in the story, I wouldn't worry about that one. I'd go worry about the dull ones that might not even be worth a mention. If smiling and nodding is the utterly typical and expected reaction, then maybe it's best to just let the reader assume it.
One last bit: Gestures might be culture specific (or a result of the way a particular character was trained to respond to certain situations). Even something that might seem as natural and obvious as smiling and nodding can actually be an unconscious assumption. Not everyone actually does it in the same way or in the same types of situations. Make your individuals individual, and you'll eliminate a lot of unintended redundancy. Where an average westerner might nod, some folks from Asia might bob their head side-to-side, and a certain physics professor I once knew would vibrate with nervous energy while avoiding eye contact. You probably don't want to a gesture that's so extremely outside the norm that it distracts from the moment, but having people respond in slightly different ways can make them more interesting, especially if those differences can somehow revealing a bit of who they are.