#2 It does not contain the upgrades we saw in Way of the Warrior.
I presume you're talking about the retractable/deployable weapons? IE, the weapons that aren't ever seen on DS9 unless and until they're needed and thus activated and thus exposed.
While it would be awesome for them to be shown, it makes perfect sense why that wouldn't be. They're only visible 0.1% of the time: when the station is in battle. So basically a handful of times since we first saw them in Way of the Warrior.
If we're going to lament things like that, we'd have to lament the lack of actual docking clamps and runabout landing pads that lower and raise and a lot of other little tiny things too...
Hey, that would be great!
I know the photon torpedo launchers extended, but the circular base is permanent. Just thought they could be seen.