I’m going by Memory Alpha with the four.
Always a bad idea...
Deck 5 is a bigger problem than 6.
Absolutely. The "To the Death" reference more or less establishes that the heroes accommodate their Jem'Hadar guests there. We see the deck is full height, with corridor branches, and we hear it has "sections". Deck 6 as described in the Okudagram has only one potentially full-height facility listed, the Brig (or a Brig), and nothing listed was ever seen; this could be a crawlway for all we care, and not really contradict anything.
Deck 5 in the 'gram has Engineering, suggesting Deck 6 would be the lower parts of the engine cowlings. Given how big the ship "really" is, this is IMHO preferable to Deck 4 being the bottom of the main hull and Deck 5 the pontoons.
The Defiant’s aren’t round, but now you have me thinking about all those round windows on the smaller Jem-Hadar fighters, too. Were they supposed to be as big as the Enterprise??
There we have yardsticks, which are consistently poor: a Klingon BoP, say. Or the TMP Orbital Office flipped to Wrath of Khan orientation and used as a starbase. But we also have the partial build from "The Ship", suggesting much smaller size.
The small windows of the
Defiant are on the inward, canted sides of the engine cowlings. A perfect place to argue that they are not at eye level (where they could only ever provide vistas to each other!) and aren't necessarily laid out one row per one deck, either.
I don’t imagine the producers settled on anything, then changed it. I’m mostly wondering what the ship makers were thinking during that first constructing/rendering when they added the windows. That initial vision at the point of creation.
That isn't the initial point, though. The initial point is the scale-less Maquis/Bajoran ship with fancy cheek and bow pods. The makers were doing some thinking when trying to turn the cheeks to escape pods and the bow to the bridge, then doing some rethinking; it's not certain if the folks who put the windows on the exterior were even informed of the stage of interior set design, or just given a carte blanche of Starfleetizing the exterior.
I think it packs shuttlecraft.
We see two types: the pods introduced in "Destiny", and the probably only marginally larger
Chaffee of "Sound of Her Voice". Tech Man blueprints give separate drop bays for the former, but there could just as well exist an internal hangar with the single round ventral door. The latter would give ambiguity and the ability to pack more than we are shown.
Why give the ship two types with basically the same capabilities, though? The pods have warp in "Destiny". The
Chaffee is probably on board from the get-go, too, its imaginary version propelling Sisko and Bashir to fictional safety and having an aft rather than side hatch in "The Search". Could this be taken as a sign that the ship has dedicated berths for just these two (perhaps three) craft, rather than a generic hangar? That is, the Tech Man interpretation?
Timo Saloniemi