There's no universal rule. It depends on Emirates' conditions of carriage. In my opinion they are perfectly entitled to prohibit break of journey, although to be fair there is a strong moral case (if nothing else) for saying that they definetely should make this clear when you buy a multi leg ticket.
My advice is that if in doubt ask the airline, by post, or email. Insist on a written response and carry it with you when checking in at an intermediate airport. You're unlikely to be bothered to read the conditions of carriage in full, and you might miss the part that prohibits break of journey (if there is one) anyway.