Yes.... as they end in "S", we just know if it is singular or plural when we see the article or the context. O lápis é meu / Os lápis são meus.
Because it is incorrect. Have is not an auxiliary verb in this case, so you can't just change its order to make a question. You must use do as an auxiliar verb: How many pencils do you have?
I think that you are incorrect in this, in British English, at least. The habit of reversing the verb and its pronoun is as common as is the French practice. Consider: 'have you time to do it?'; ' have you any money with you?' The auxiliary 'do' is, often, a requirement, but by no means is it so in all situations.