It would be a bit easier to understand if it starts off with 영어로.
영어로 할아버지를 무엇이라고 합니까?
In English, what do you say when you refer to "할아버지"?
할아버지가 영어로 무엇이라고 합니까? sounds like "What does the grandfather say in English"?
이/가 has the subject and the action interconnected together while 은/는 doesn't.