Hm, maybe, but in my experience qualis on its own usually refers to character, where people are concerned. I can't remember any instance of qualis est? meaning "What is he like physically, what does he look like"? and, taking a quick look in dictionaries, I couldn't find any example there. For now, if I were to ask "What does he look like?" in Latin, just to be on the safe side, I would clarify my meaning by adding aspectu, habitu or something like that. Now, of course, maybe the person asking qualis est puer? is asking that in a very general sense, so that it would be OK to include information about the boy's appearance in your response, but the person asking the question perhaps also expected other information.
Have you read that question somewhere, or are you actually wondering how to ask it yourself?