Could an adolescence boy who had hypogonadism (due to malnutrition) catch up his growth (genitalia, height etc...)after he has recovered while he is still in puberty?

Many of the negative effects of malnutrition are reversable, some not, depending on a number of factors. Potential for increased stature depends on whether growth centers are open, but most close in males between 16-18. A single x-ray of the wrist/hand can see if they are closed. If so, no increased height would be expected. Gonadal change would vary. Puberty may be minimized/ended by malnutrion