It's a problem. While I've been editing and 'trying' to balance the ST and SG ships the problems of Nukes comes up often. If a weapon is very powerful, say like your 2800 Quantums they tend to allow for 'bleeding damage' or 'critical hits'. What this basically means is that depending on how fast the aggressor and defender are travelling and how fast the projectile is, some weapon damage passes through the shields and in rare cases all of it.
In a game where say an Intrepid has a hull strength value of between 15-20,000 and then has ultimate recharge shields. There will be a fierce battle to drain shields and gain a hull hit, but when that does happen, the weapon can unrealistically obliterate a ship.
Also, another thing to consider is 'damage radius'. If on your projectile this is set to a value such as 0.1, on a hull impact the photon will do the named 1400. However, increasing the radius causes more damage, both as a form of damage multiplier and if the impact radius affects other system ie. the shot damaged the hull, warp core, shield generator and sensors, the damage taken is also much greater.
On the Stargate Hiveship, one Nuke currently does 10% hull damage, but if that nuke detonates around the area of the ship where the Power Generators are it can raise up to 25%.
I'm with you on the subsystem damage. On my install my Intrepid has a hull value of 20000. I've balanced the hull strength according to the ship size and then take into consideration the technology level. In a lot of battles ships can take a lot of hull damage, it's when a subsystem is targeted/affected that problems arise. This can be seen in battles such as the first encounter with the Breen in the Dominion War. Once all the ships were disabled, they took a good deal of Torpedo damage before the ship exploded.
The Lakota may have been an old design, but that ship was pretty heavy. I supposed an analogy would be driving around on a push bike with anti tank missiles welded to the sides, at the end of the day it will still blow up tanks. In that battle though the Defiant was still clearly in a league of its own, and they weren't really trying to blow it up. The Defiant has immense fire power, it's not unrealistic in my view to have it level out with a Galaxy at all.
I think though, that the idea and strategy your applying to you install is brilliant, but I don't believe it to be canon. In the Trek battles, ships simply didn't have the ability to recharge their shields to 100% that quickly. Early episodes of Voyger like 'Basics' had hit and run tactics from the Kazon attacking a single shield vector to drain it. The ship couldn't just recharge that area. I think I'm right in also stating that in numerous DS9 episodes such as the finale, once the Dominion broke away from the initial fight and regrouped at Cardassia there were hours of waiting and when the Defiant was giving a tactical update, their shields were still pretty low.
