Lol, with a destroyer that has good firepower and armor with weak ass subsystems pitted against an enemy that uses direct fire beams, hell even versus slasher beams that's a problem. A weak subsystem versus a direct fire beam is just deadly. What do you think most direct fire beams target? Probably the really powerful turrets on other capships, or the meatier and tastier subsystems.
Perhaps a new hades being developed could make a balance on stronger subsystems and less armor. But the hades itself is already extremely unique and even sought after in the community. If integrating shivan technology, it's reasonable to assume gti was looking into reproducing energy shielding for their destroyer. In the least at perhaps they were trying something cool like using energy shields on subsystems in place of hardening subsystems with depleted uranium (force field isolation happens all the time in star trek, i don't see why you couldn't do something like using something as crude as a fighters shield generator around a subsystem). If you did use a shield generator around a subsystem, it'd probably offer no more protection than depleted uranium does since disruptors do cause shield damage (a move like this would replace something clunky and old with some just as usable, bot more efficient...sort of like getting rid of IDE interfaces in favor of new and smaller SATA, in the beginning SATA was no faster than IDE, but it was something that could be improved upon, and as time goes on shielding gets more advanced and more resistant). The final mission of silent threat when you take down the hades was when the hades was being brought online.