"why are there...?" is a direct question. "Why there are..." is statement posed as a question. For example, "why are there so many people in the restaurant?" You don't know the reason and therefore you asked the question. "Why there are so many people in the restaurant" is a statement asked as a question. You already know the answer but wanted to see if the person you spoke to knows the reason as well. It's more of a rhetorical device.