Initially, I liked this idea. It's reminiscent of a minecraft mod, Big Reactors, which added multiblock reactors and was very well received, and I myself loved for my adoration of logic and spatial puzzles. But I do have my own concerns. I am sorry for the wall of text.
I know it was said earlier than the 'no interior = More systems = better ship' is not desirable, but I would like to point out that this argument isn't helpful. In real life the same thing is true as is in starmade; if you use room for interior decoration instead of for practical application of active systems you end up with a mechanic that does not operate as well as that of the practical application fill. Thus, while I too hate the meta of 'fill all the gaps' I have to say it's only logical to conclude that it is not just to punish those who want stronger ships, sacrificing internal decor. I enjoy my internal decor and knowingly (and gladly) make that sacrifice. Is it preferable to have a weaker ship that looks good? Objectively there is no answer, but the choice must be made by the designer. Why punish one and reward the other by reworking energy in a fashion that bottlenecks the application of an operational efficiency based starship over a livable or pretty one? I do not see this as an improvement, but as a leash being applied to people who wish to milk efficiency. This only accomplishes punishing one type of player for the choices of another, unless you leave the option for efficiency milkers to pull ahead of internal designers in some fashion once again, which is clearly a point of contention. Low hp no armor blocks, even for internal buffering, are useless against most systems and I am brave enough to suggest that many players would agree with that. It's simply not a viable trade off, unless the desired outcome is to turn Starmade into a little less 'Design and battle!' and a little more barbie fun house. I like my barbie fun house, but I like it in context of the game as it is.
Additionally, while I do approve of work to improve the fundamental principles of the game, I am concerned about the approach of this idea. Conceptually it is a kind thing and clever to be sure, but the applications of coding alone make this a boggling take-on. Heat detection sensors between all modular systems and ships, heat counters, let alone the result of reactor breaches on multiple ships at once? The coding would be a very impressive undertaking, but the burden on a server or even client-side would skyrocket quickly if you are winning a battle; why punish someone for victory? While it could be argued this is already present (and it is to no fault of anyone) many PC's struggle with the workload now.
This system would offer things like effect module (cooling) or the like a chance for entrance and would offer an exciting change for star heat I admit, but it also opens other avenues. Shouldn't beams create more heat on targets than a cannon? Should there be effect modules in contest of these systems? When looking at a larger ship with laden armor and tons of turrets, would it not simply just be most efficient than to find a way to overload their reactor than to bother trying to out-and-out fight them at all? What's to keep anyone from just using the layout of a ship to say 'Well logically if that ship were an empty skin hull, I would put the reactor riiight... there.' Boom. While innovative, this system would offer an entirely new kind of meta. It's fine and dandy when Worf is targeting a Romulan power reactor or a thruster cluster, but in practical application, no amount of shielding will keep any tenacious fighter out of the hull breaching tactic. Reactors will become less of a 'benefit' for ships, and more of a hindrance, leading to bulkier, slower, and far more viciously defensive ships than the current system which allows just a hint more flexibility. I, for one, would make it a point to just punch shields down with Ion and then set punch-through cannon waffles through hulls playing where's waldo with a reactor. Marco, Polo. Marco, boom.
My final issue (insofar as being logic goes) has already been mentioned and I feel deserves emphasis. We have a fleet system now, and we have turrets. Who wants to design one of these reactors for every last ship and turret of middling size? The idea is, in itself, a bit of a turn-off to the idea of using the more-or-less recently implemented fleet system at all. I agree the current system is flawed, but is this sort of complication a necessary one? It's a good brainstorming step at the very least, and brilliantly creative at best, but is it necessarily an improvement?
I don't like the idea of spatial heat and spatial multi-structures being used in conjunction with weapons based systems in a hull skin, but I have no logical argument to present and recognize that now to confirm my bias, as is only fair. The idea reeks of star wars 'Heat vents' to me, and we all know how the death star worked out. I'm not saying I mind my ship having a glaring weakness, but all ships having the same weakness in likeness? If vents were not included, why not? When dealing with the vacuum of space it seems rather reasonable to use such a simple mechanic. But then we could also hit meta-venting and modular issues regarding vent placement an-- GUH. Anyway, not entirely logical, this bit, but had to vent. Ironically.
Just my two cents.