I have a feeling in a post-apocalyptic wasteland that being ugly is the absolute least of your problems. plus the amount of medicine and materials needed to do it would be a waste.
I meant more as a courtesy to those of us who can't open up the commands and change it. They had the ability to change your "look" completly in FO3 and presumably the ability is there to do it in NV because the dr. that fixes you up in the begining of NV apparently wanted to know if he got everything back in the right place. ie. nose, check, ears, check, two eyes, check, hair color, check.
Even if the materials needed would be a waste and all that, I would rather have the option to do so from a roleplaying perspective and the changeable nature of my character. Make sense or not, its one benefit that should not have been cut in my opinion.