Most military reactors are small modular units as opposed to single larger ones. In a warship especially it would be better to have redundancy against power loss. Still on the other hand the efficiency of the reactor should increase with size. This is reasonable as there are fixed elements that you need regardless of the size (cooling, controls, support services) and though the do scale with the power output they aren't linear.
So the power per hull space should increase per hull space of the reactor since there is what amounts to a fixed overhead cost plus one that rises far less quickly then the power output.
The question is how to model this mathematically. (1-(Fixed Cost - Efficiency Reduction per HS * (Reactor HS-1)))*Total Power Out Put I think works.
If you say set the Fixed Cost at 30% and Efficiency Reduction per HS at 0.5% for a reactor tech with 3 Power/HS you have:
1 HS reactor: (1-(.3))*3 = 2.1 Power
5 HS reactor: (1-.28)*15=10.8 Power compared to 10.5 Power of 5x1 HS reactor.
This produces non-integer power outputs though and that is not so easy for the player.
Three things seem easier to do to make things interesting.
1. The first is to say fix the crew at a per reactor basis with only a small increase for size. So a 1 HS reactor takes 5 crew, and a 5 HS reactor takes 7 crew. So you need 25 crew to support 5x1 HS reactors compared to 7 crew for a 5 HS reactor. This is reasonable since the reactor isn't more complex to run or repair.
2. The second is to give larger reactors a bonus in power. +1 Power per 2 or 3 HS. So a 1 HS reactor would produce 3 Power, but a 3 HS reactor would produce 10.
3. The third is to increase the HTK of the larger reactors in a similar way as the power so larger reactors are intrinsically a bit tougher.
So larger reactors are more crew efficient and produce slightly more power per HS but still end up with integer numbers of power but are less redundant though slightly more difficult to kill then a comparable number of smaller units.
This gives the player choice I think. For some tasks larger reactors become more appealing but you have to balance that against serious energy losses. My feeling is that military vessels always will have multiple reactors but at least in this case they won't always use just large numbers of 1 HS reactors.