Not to play the instigator here, but, I am looking at this with an open mind. Magic is a tough subject to touch upon, because, hey, its magic. But, I feel like overall its relatively well touched upon. I understand that there are going to be little inconsistencies, or things that need to be better explained, but, I am looking at this as though it were through DnD or another like genre game. Perhaps like World of Warcraft, in the sense of runes and gems.
Large structures, the E.U. ships, require the runes, gems, and the manafusion reactor in order to create the shield. The Runes are probably the most sensitive piece of the whole kit and caboodle. One scratch, well, one that is deep enough I suppose, and the shield goes down, or, a section of it. The runes are like relays, along with the gems. They allow the power from the reactor to be manipulated into the form of the shield over the hull of the ship. The have a finite fuel/charge amount, much like a Mage’s mana shield in WoW.
When the shield is static, it draws power are a rate that can be compensated with your fuel stores, possibly even natural regen rates. Going off of WoW logic, coupled with DnD. Yet, as incoming fire comes in, it takes mana to keep that shield up, the more “damage”, the higher the expenditure. So, ergo, as the first attack comes in, the manaforge spools up, outputting the energy/mana required to not only dissipate the energy from the weapon impact, but also keep the shield up to the current level as well. But, therein lies the problem. I think it is fully fair to say, hey, we focused a ton of our R&D on shield strength, on the ability to dissipate large amounts of energy, but, as a drawback, they can only operate for a certain time, before being completely spooled out.
Which, brings up the next question, if you run your manafusion reactor to high peak level, and run out of usable mana, does that also mean your ship is dead in the water, let alone without shielding? So, Duck has a strong front strength, but, coupled with several key weaknesses. The runes and gems are key to the shield. Damage even one, and everything goes tits up. Yes, they are defended well, but, even a momentary lapse in shielding, say, from a massive kinetic blow, or something else, could in theory knock something loose, or even damage them.
Likewise his fuel, it is pretty much only refined and made in his home territories, and if he is unlucky, only upon his capital, or a few select worlds. The fuel rods, imbued with magic, have a finite half-life. They can power the systems, but, if the demand is too great, then, more than likely, they burn out, and will need to be replaced, dropping usable power lower. It’s a give and take. And the increased heat is like all reactors, you can overheat them to gain more power, pushing them past safe levels in order to go above the normal 100% usable power. But, that damages the very reactor itself, perhaps not on a large scale, but, it does take its toll. And it makes sense when ships get so large, they will have more than one reactor. Like boilers on steam powered ships up until we figure out how to use diesel and so on. Or like todays nuclear powered vessels, they have more than one reactor in order to use one, while resting the other.
Which leads into the final part, the strength of the shields. Single ship to ship combat, you can last longer. In a pitched fleet battle, with capital class warships, fights, gunships, etc, it all depends on how much of a beating you are taking. Ten ships targeting one at the same time, well, shields would probably overload/go down after the second volley, or be very close to failure. You have it so you can throw a good punch, fire some heavy hitters, take that first punch, or two, or even three, on the chin, but, then it’s a matter of tactics and so on.
We all have little quirks. For instance, Wilson’s dreadnoughts, they could in theory just ram the E.U. ships, regardless of the shielding. And while the other races right now do not understand mana, there is no doubt places that are utterly devoid of magic/mana. The E.U. is powerful due to their magical affinity, but, on that same accord, they are hamstrung by it. They heavily rely on it. Without it, well, they are still able to operate, but, at a great disadvantage.
This is all conjecture, please feel free to correct me where I have gone astray.