They aren't added because using them would be a no-brainer. Every cargo vessel would have them, there's no decision making involved. You get the admin bonus if you set up your admin structure right and you get the ship commander's bonus on top. It's the same reason why there isn't a terraforming leadership module or Sorium harvesting leadership module.
Seems like this is an unpopular idea, considering all the thanks you're getting for shooting me down 
, but I feel compelled to disagree regardless. First, so what if every cargo ship has one? Let it happen.
It is important to recognize that one of the core design principles of Aurora (articulated by Steve himself) is that good gameplay features create interesting decisions. If adding a feature doesn't create an interesting decision for the player, it's just an extra button to click to get +X% bonus or whatever. This is the reason why the suggestion of additional officer modules for commercial ships has never happened, because it does not create any interesting decision besides "when do I spend 5k RP to research this?" and "How fast can I double-click to add this component?" -
or at least, we generally perceive this to be the case.
Every cargo ship (probably) has shuttle bays too, does that mean they're a nonsense concept?
Cargo Shuttle Bays present an interesting, if minor, decision in the choice of how many to add. Each additional one improves your ship's load/unload speed, but also increases build cost and ship size, so it is a proper decision to make about how many shuttle bays to have on a ship. Admittedly a minor decision but it is there and is not what most would call a "no-brainer".
Same for CIC bridges on combat ships; that tactical bonus is an absolute no-brainer, on any ship larger than an FAC for 3 HS. Are those too much, as well? After all, you get a pretty good Tactical bonus from setting up your Admin structure correctly there, too, if you emphasize the trait. Why even have that, if that's an issue?
The CIC isn't really a no-brainer, either. It might seem like it, but consider two extremes: on one hand, if a ship has only one weapon mounted, it is probably better to mount a second weapon to double effective firepower than to mount a CIC for a smaller boost to effective firepower (
vis. hit rate). On the other hand, if a ship has 100 weapons, a CIC will almost surely provide a better effective firepower improvement than mounting the 101st weapon for a measly +1% firepower increase. These cases are quite obvious; the question is in-between, where is the optimum point where a CIC is better than an additional weapon (or other component)? This is not so trivial! We have to consider not only the above balance but also other factors, such as opportunity cost versus other components (that 3 HS could be used for, say, a Main Engineering, a bigger sensor, or some hangar space for a small scout shuttle) and expected benefit based on quality and availability of officers (if you don't even have enough officers to staff your ships with just Bridge + AUX modules, you may find many CICs going unstaffed! Of course this depends on how you design your fleet and how you manage your officers...), so this is not even a mathematical optimization problem but a true decision-making opportunity.
The same logical problems apply for the other existing command modules (ENG, SCI, etc.). If I only have 2-3 survey sensors on a survey ship, a SCI module may not give as much benefit as an additional sensor, for example. These are problems that would not really apply for commercial versions (giving bonuses to Logistics, Mining, Terraforming, etc.) - commercial ships are simply so large that a small officer module would be comparatively a no-brainer - what is 150, 250, or even 500 tons for a +10% or better boost to a 125,000-ton terraforming station, for instance? It's a trivial addition, unless the cost of the command module was so large as to break roleplay and immersion for the sake of "balance".
Second, if it's really a problem to have a named Cargo officer on every Naval cargo ship, instead of just implied. . . then instead of dismissing the notion completely, let it be large or expensive enough of a module to have a tradeoff. If it's, say, the size of a cargo shuttle bay, until you already have 4 shuttles, adding one or two more gives more than 25% logistics; you'd need a bunch of really good logistics officers to justify trading a shuttle bay for one in smaller ships. That way, only your heavy freighters built out of extremely large shipyards merit the office. Or same/same for large missile boats, stations, etc. - those may have a cargo officer, but your family-owned small freighter doesn't have the dime for such fancy things.
This part is a valid counterpoint, however. Personally, I'm not sure there is much need since this functionality essentially duplicates the Cargo Shuttle Bay functionality with a variable for officer skill level, so I doubt Steve would ever feel inclined to add it - but at least if he does consider it, this argument demonstrates that it can be an actual decision unlike most of the suggestions we see for things like Mining or Terraforming officer stations.
