Would the redesigns affect the hull shape, though? Hulls seem sacrosanct in Trek: ships like Voyager apparently won't move properly unless Kazon suicide boats or the holes left by them are patched up. Redesigning the exterior of a starship might be major work, quite possibly not worth doing for that extra 15% of combat agility or whatnot.
I'm with Timo
on this, I'd always kind of assumed the hull shape was the same, but filled with very different contents.
For example instead of science labs there would be rows of bunks for troops, combat training facilities alongside Holodecks redesigned for troop training more than leisure, and more stock of torpedoes and war materiel.
The hull could have been largely sketched out for years, and the windows etc. left in as they were no particular detriment to combat performance...