Shield generators make perfect sense in a "military" compartment. We can already slot Shield Cell Banks and Guardian Shield Reinforcement packages in military compartments, so the shields themselves would naturally belong.
I think though that the reasoning behind these slots is actually "reinforcement", as the only available modules are hull and shield reinforcements, with shield cell banks being counted as reinforcements.
If that is the case, then I vote either call them "reinforcement compartments", or else keep it under the general title of "military" and allow us to put shield generators there.
I like the idea of using military compartments at reduced size for non-military modules, but I wouldn't know if that would exceed the advantages Frontier factored in for those ships, to the point of overbalance.
On that note, I'd really like to know what sort of system (if any) they use to determine how many modules of what size are allowed for each ship, and if they use a points system to balance things out.
For example, each ship might have 100 points. Any positive aspect would reduce the points, and any negative aspect would put points back, and they can play around with options until they hit zero.
If that resembles how they configure ships, then I don't know if this idea would bring the balance into the negative.