I had one from last NYDH that had trouble hatching, but did manage to hatch on her own. But she always acted cold and peeped ALL the time. She ate, drank, and played with the others, but never seemed quite right. At about 3 weeks I found her just dead in the brooder. I had done everything I possibly could to get her better, but there was just something wrong that no amount of good care was going to fix. That's just the way it goes sometimes. It is sad, but you can't always save them, no matter how hard you try.
I put my chicks on pine shavings as well. They peck and play keep away with it, but I've never seen any actually eat it. IMO, a normal chick who has access to feed isn't going to consume enough of something like that to kill them. If they did, they'd never survive in the wild. There are far too many toxic things they could gobble up and die from.
It's possible the cedar could have caused him complications. But I think I would lean more toward him having something not working right inside. If he didn't want to eat much, it is possible his gastrointestinal tract didn't "finish" or was messed up somehow.