Mostly on the Bungie Universe forums people are arguing what ships are operable for atmosphere transition and travel. So I am going to make a list of what I know, if anyone would like to contribute please, help.
I have not seen in any video or book that describes or shows a Destroyer in space, though I would imagine they would as they are the heavier cousin of the Frigate. Though the Halcyon is a big problem as the ship has been described in Halo:The Flood to not be rated for atmosphere. (Help please Frank!!)