This idiom is usually used to challenge someone who is not answering your question. For example: a teenager comes home an hour late at night. His mother asks him where he was, and he doesn't answer her. So she says, "Don't you have a tongue in your head?" She is asking him if he can speak or not (you need a tongue to speak).

They is also an old English saying."Has the cat got your tongue" (The cat of nine tail was a whip used on British sailors in old days.