Could just be that, since most if not all ships come from blueprints (post-collapse era tech), and the only instances of actual, professional bp modifications were extremely expensive which required specialized knowledge that most of the sector simply lacks nowadays, then it's simply not worth it to do it for an entire line of battlegroup ships.
There's also the fact that we seem to lack the proper knowledge on how such modifications were done to begin with, and the few examples that survived both the 50 years journey and the subsequent 2 AI wars are just too precious to be torn apart for study.
Finally, the Hegemony seems to be doing well enough with mostly regular lowtech fleets, so why bother with slightly better versions of those, really.