Nothing wrong with the lad taking pride in his appearance and personal hygiene.
This is the time when his hormones will be going funny and his body will be changing. He should be allowed to make himself feel more comfortable - he'll be learning how to interact with his peers and the opposite sex over the next few years so, anything that helps him to become a confident young adult can only be a good thing.
As long as his school work is good, his uniform is smart and his shoes are polished, the school, in my opinion, should lighten up a bit.