I think infertility can sometimes be a problem with untreated or undertreated males, so I don't believe the hc treatment would have a negative impact on that.  As far as the changes in appearance of your son's genitalia---that would definitely be something I'd point out to his doctor, as increasing signs of androgenism would point towards undersuppression. 

The amount and quality of pubic hair (e.g. how it has spread; fine vs. coarse; etc.) helps the endo assess which stage of puberty your son is at.  Increasing penis and testicle size is also an important measure of adequacy of treatment.