Appetite suppression as a side effect of stimulant medications is common, and most of the time it is inconsequential. However, in children of small stature, particularly those who already are on the picky end of the spectrum when it comes to eating, weight loss (or failure to achieve adequate weight gain) can result.
It sounds like your son's diet is pretty deficient in protein intake, so it would be wise to try to increase the range of protein rich foods he will eat. Consider soy-based products that can be used in milkshakes. Some children will accept these, and they can both taste good and be nutritionally sound (without being rich in sugar and dairy fats). Also, you might consult with a nutritionist. They often deal with the sort of dilemma you're facing.