How does having a hypertrophic cardiomyopathy affect a child's development, will they be small for his age?

No. Your child will not necessarily be small, but he needs to be very careful s he exercises. Too much exercise can overload the heart. Be sure that your pediatrician refers you to a pediatric cardiologist to help with your child's care.
Possibly. If a child is diagnosed during the first year of life, the prognosis is not as good. They may be severely symptomatic and can have impaired growth. Hcm associated with syndromes may also be associated with poor growth. The majority of children, however, will grow normally and appear to be remarkably healthy and robust in spite of having a serious heart problem. Competitive athletics aren't allowed.
It depends. Genetic syndromes like noonan's and what used to be called leopard are associated with hcm and small size but they have other physical characteristics that are clues for the pediatric cardiologist or pediatrician to refer to a geneticist. If these are not present, my local pediatric cardiologists tell me the kids can grow normally with proper care. Ask your child's doctors if you're concerned.