How old is your son? Did he have reflux as a baby?
My son has nodules, too. He's almost 4 years old and had severe reflux as a baby. He was on Prevacid until about 9 months of age when we assumed the reflux was over (that was the age he stopped spitting up, and he seemed fine after stopping the medication.) He's always had a hoarse voice, and when he had tubes put in his ears, the ENT also looked at his vocal cords and found the nodules. He has just started speech therapy, and the ENT suggested we restart the Prevacid. He said it's really hard to determine whether or not a child has reflux, but the medication is worth a try. We will also go back to the ENT in 2 months to re-evaulate.
My son is also a screamer (a whole other issue we are dealing with!), and that will contribute to the nodules. I think it is definitely worth treating. For us, I hear it getting worse and I can't imagine what his voice will sound like in a few years if left untreated. I'm thinking that once we see improvement while he's in speech and taking the Prevacid, we stop the medication. If the hoarseness returns, we know he's having reflux issues.
Hope this helps. :)