One and two are grammatically correct, indeed. But may mean different things. The stores are going to close in a couple of hours... means... they will shut in about two hours. The stores are going to be closed in a couple of hours can mean the same thing... the stores are going to be closed BY SOMEONE in two hours' time, approximately. Or it could be this... "Let's go to the shops in a couple of hours' time." "In a couple of hours? But the shops are going to be closed! It'll be too late!" This does not say WHEN the shops will actually be physically shut up, it simply states that at that time they will be closed. They might have shut an hour earlier. Closed can be a past participle, or an adjective. The stores are going to be closed by the manager... is different from... the stores are going to be closed. Substitute 'cold'.. the stores are going to be cold by the manager... NO. Doesn't work. The stores are going to be cold. Yes, does work. So closed can be a past participle, or an adjective, and which sentence you choose may depend on what you want to say!

One and two are both fine. Three is grammatically incorrect..

Or, "The stores are closing in a couple of hours."

The stores are going to close in a couple of hours.