Does the noise usually called “pipe clatter”, distinct from ‘hammer’ usually attributed to air in the pipes cause harm to the plumbing or is it just harmless noise?
Yes, excessive pipe clatter may harm your plumbing, that stress may eventually cause failure at joints or fixtures.
If it helps, I had what I think might have been pipe clatter and think I fixed it. It only seemed to happen when a particular faucet was running. I went under the sink and it turned out that the hot water shutoff was not completely open. I opened up up fully and haven’t had any noise since.