Well, so most of your ships power comes from the reactor. So, I am going to take a shot at it, and I am not trying to say one way or the other.

A reactor has a set safe operating level, I think we can all agree on that. Nuclear, magical, cold fusion, etc. You can skirt around the safeguards for a little while to boost up the power output, but at the risk of damaging the reactor, or other components associated with the reactor/core/power plant. You use your magic stores, coupled with a mechanical/magical physical device to provide the power for your shields. I would assume that the runes and gems powering the shield, and perhaps other devices are a weak point, and while they are heavily defended no doubt, even to get a glancing blow or a to damage one of the runes or gems would hamper the effectiveness of your shield. 

I take it that these components are placed in strategic locations, which would only make sense, like any other defensive system. So, over time, your manafusion reactor outputs power, but, its fuel source, magic, is at least in my mind, a finite amount stored into perhaps fuel rods, or some sort of holding device that allows the storage of mana/magic for refinement into power. Now, I am taking a guess that you have to in a sense, "mine/collect" this mana/magic for your reactors, something that at least from my educated guess, is not done on the fly, but rather at a ship yard or fuel facility. Now, when more power is drawn from the storage device, the less it has to offer as it is depleted. The reactor, as it spins up to provide more power for increased shielding or other systems, would heat up, degrading its output by a certain percentage, correct? 

So, your shields are strong, they can withstand the first few hits, but, would they hold up in a prolonged engagement? Your fuel source in my minds eye is mana. It can be regained, but, it has to be done at rest, rather than combat, or, per say, that while in combat, it regenerates slow, very slow compared to being in a calm meditative or at ease stance. Kind of drawing from my experiences with Larping, DnD, and WoW, to try and understand. I am not taking any sides, but merely wishing to better understand something as this, within the realms of our roleplay's universe. And by universe, I mean like the setting in which our roleplay takes place in. 

So, good sir, please, be so kind, and teach me some more, so I can better understand and react in a manner that creates smooth sailing for everyone.

The smaller the ship, the weaker the shield, and vice versa. Magic is your main fuel source, so, how do you get it in a usable form to power your ships and other technology? Can it be done on the fly, or, do you have to get more "mana cells" from your fuel depot? I appreciate your time in helping to better enlighten us all.