Not an expert but could definitely be neck related. When my neck used to be insanely tense I would get some issues from nodding but it’s better now and I can nod to music and such with no issue. My pt actually had me doing some head nodding and side to side movement exercises just to get me desensitized to normal movement and such since I used to be so sensitive and would always sit extremely rigid trying to never move my head.

I don’t think it could cause any damage to your brain, I mean just intuitively I don’t think there’s any way, nodding is something people have been doing for ever, our brains aren’t just flopping around all the time with no protection. It’s just not how our anatomy works I don’t think.

Ive heard that hard head banging and such like what heavy metal enthousiastes might do at concerts can cause issues because after a little while it disrupts the flow of protective fluids in our skull but again I’m no expert it’s just what I remember mark (I believe but could have been someone else) telling me a while back. But there’s a whole world of difference between nodding along to a song and violently head banging while going crazy at a heavy metal concert.