I have never seen anything like that. The bumps look inflammed and possibly infected inside, like pus pockets. I also don't like the blackened areas of tissue around the base of the beak. Bitten by poisonous spider maybe, other bug bites? No idea really.
Edited to add: Agree with Pwand, you might consider treating with antibiotic's, though the way that chick looks I don't think he's going to last long.