Was the battle of Wolf-359 featured in DS-9 as well?... since I didn't watch that show. If it were me (painting for myself) I would only use the lifeboats from the Galaxy Class / TNG-era ships; the boxy ones. But, again, I wanna cover all the bases.
It was seen in the pilot episode as part of Sisko's backstory. (Both he and his wife were involved in the battle; his wife got killed.)
I was always under the impression that the squares on the Ent-D were hatches covering the real pods, since that's how the USS Voyager handled it:
Star Trek Mechanics and the Star Trek Fact Files has photos of the pod filming model and diagrams, respectively. Both pics can be found at Bernd's site.
And here's the images: