Midway has gone through numerous refits over the course of her service history. Stuff has been added, then removed, and in some cases put back again. For example, when they gave her an angled deck for landing, they also installed a small waist capapult to launch planes from mid-deck. When the jet age bcame firmly entrenched, this catapult was incapable of launching the heavier jet planes, so the waist cat was removed and the two bow catapults were upgraded. Midway would never be able to launch F-14 Tomcats, but would serve well as a base for A-7s, F-8s and eventually the F/A-18s that replaced them both (and which outlived the Tomcats). Ironically, the Tomcats would be the planes that had to be modified to attack ground targets later in their lifespan, since no one flies anti-ship planes anymore, and the 18s were built to do basically anything you need a warplane for. Midway was small compared to the newer Nimitz class ships, but she was able to deliver the same kind of punch that her descendant ships could.
There used to be a ton of .50 cal gun points all over the place; there were removed (along with all the original 5-inch gun armament) as missiles pretty much ensured that no plane or hostle warship would be able to get close enough. Fittingly enough, in the 1990s most warships put more .50 cal guns back on, to defend against the tiny, explosives-laden suicide boats that various groups could throw against them. More fun still, stuff often gets recycled between ships; the recently-decommissioned USS Independence (from the 1950) had one anchor and both anchor chains moved over to be used by the brand-new USS George HW Bush, which gets commissioned next year.
I see no reason that Starfleet would add, pull, and then re-add stuff as necessary. At some point in the future, the fancy phaser strips could be replaced by upgraded ball turrets, photon torpedoes could come back in vogue, and the command colour would finally be blue...
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