The Washington St. Ale house used to have a deck but they built it in to create more indoor seating. Shame, we enjoyed it.
Minus the rudeness of the passers by, walking up to the deck and asking for cigarettes or even one time some guy asked the 2 ladies next to us for a drink of their water. Unbelievable...
Houlihans by Christiana Mall and Friday's on Concord Pike have decks but I'm not crazy about their food.
Iron Hill on the waterfront is nice, but limited typical beer choices due to it being a micro brew.
One place that is out of the way and a bit fancier than what you are looking for is
The Half Moon Resturaunt in Kennett PA. It's actually called 'rooftop dining' vs. a deck but still enjoyable, especially in the late in the evening into night (bring your sunglasses for the setting of the sun). They specialize in out of the ordinary cuts of meat. I really enjoy the Buffalo burger (Buffalo the animal, not the wing sauce). Also over 27 types of beer.
Come to think of it, probably not the best place to bring kids. More suited for couples.
Ok, so after thinnking about it, it isn't what you are looking for but still nice and worth mentioning. I digress...