If u want to ask if he has One brother, you would ask 'hey, do you have a brother'? notice 'a' --> 'brother'.
But if u ask the question using ' How many brothers do you have?', your question is already assuming the word 'brother' as a plural form, since u used 'how many' at the start. If 佢 only have one, 佢 will reply 'only one' but if he has 2 --> or more, he would just reply the number, e.g. two, three...etc.