In older releases, I would use Military Subsystems as a cheaper Augmented Engines for civilians, but the interaction with DP limits from skills and XP gain depending whether or not the ship is military in the current release muddies up that decision. Most of the time, I prefer to keep civilian ships civilian, even the fighting ones like Atlas II.
Eh briefly in terms of XP gain, it doesn't matter if the ship has Militarized Subsystems or not. Civilian ships with the actual "CIVILIAN" hint in ship_data.csv get their DP cost in terms of XP divided by 4, but it doesn't matter whether or not they have weapons nor what hullmods they have. For all other ships, then it's if they have weapons or not (if they have any weapons, including fighters, then they count for their DP, but if they don't have any weapons, then they count as DP/4 for XP purposes). So the Militarized Subsystems hullmod isn't going to matter.
The list of ships with the "CIVILIAN" hint are:
Mercury
Hermes
Dram
Ox
Mudskipper
Buffalo
Tarsus
Valkyrie
Phantom
Phaeton
Salvage Rig
Nebula
Starliner
Colossus
Revenant
Atlas
Prometheus
These ships always count as DP/4 for XP bonus purposes, regardless of if they have weapons. Note that Atlas2 is a different ship than Atlas, and so forth with the other modified civilian ships. Also Mudskipper2's skin removes the "CIVILIAN" hint so it counts for full DP value as well.
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I sometimes put Militarized Subsystems on my civilian ships for the sensor bonuses, since I tend to travel with 2 Atlases and a Prometheus as support ships, and that allows me to see enemy fleets from farther away (especially with High Res Sensors) as well as make my fleet easier to hide. Otherwise, I put them on stuff like the Atlas2 so that it can get the various combat bonuses. I think putting those on converted civilian ships sort of emphasizes that those are converted civilian ships, not full-on military ships. Even if some of them (like Atlas2) can perform better than military ships.