Guess today is my day to post wall of text posts. There's been a lot of threads roaming over various aspects of ships and the Third Imperium setting that have prompted me to want to put down my thoughts more centrally, where they are the actual topic of the thread and not derailment
So this thread will have a bit of setting speculation, then I'll actually get to the point about how I think merchant ships would actually be built, unlike the adventurer specials that are generally published. Of course, adventurer specials are what we need as gamers. No one is suggesting the PCs play literal space truckers who live normal lives. 
The merchant ships in the core rules and high guard are generally designed for player characters and free roaming sketchy tramp traders in general. They are sort of jack of all trades ships with additional capabilities and lack of specialization that commercial ships would likely avoid. Commercial businesses are quite focused on cost efficiency. They aren’t going to pay for civilian grade sensors instead of basic sensors unless required by law or minimum safety. They aren’t going to have weapons unless they pay for themselves in quantifiable reduction in lost revenue. And so on.
The problem for ship designers is that there are a lot of unexplored elements of the status quo, which means a lot of how ships are designed will be determined by the assumptions each particular table makes about how the setting works.
For instance, how common is piracy and how does it work? Do pirates attack ships often enough to be a concern? And, if so, do they do so in ships that a merchant could reasonably fight off if armed? When they do attack, are they just stealing cargo if the merchant surrenders? Or are they stealing the entire ship and/or killing the crew and passengers? If they just steal cargo, merchants aren’t going to bother going armed. They’ll just have insurance and surrender as soon as it becomes apparent that escape isn’t possible. If they steal the ship, is it ransomable for less than the cost of effectively arming the entire fleet? If they are murdering people, is it even worth going to that area at all?
The merchant ships in the core rules and high guard are generally designed for player characters and free roaming sketchy tramp traders in general. They are sort of jack of all trades ships with additional capabilities and lack of specialization that commercial ships would likely avoid. Commercial businesses are quite focused on cost efficiency. They aren’t going to pay for civilian grade sensors instead of basic sensors unless required by law or minimum safety. They aren’t going to have weapons unless they pay for themselves in quantifiable reduction in lost revenue. And so on.
The problem for ship designers is that there are a lot of unexplored elements of the status quo, which means a lot of how ships are designed will be determined by the assumptions each particular table makes about how the setting works.
For instance, how common is piracy and how does it work? Do pirates attack ships often enough to be a concern? And, if so, do they do so in ships that a merchant could reasonably fight off if armed? When they do attack, are they just stealing cargo if the merchant surrenders? Or are they stealing the entire ship and/or killing the crew and passengers? If they just steal cargo, merchants aren’t going to bother going armed. They’ll just have insurance and surrender as soon as it becomes apparent that escape isn’t possible. If they steal the ship, is it ransomable for less than the cost of effectively arming the entire fleet? If they are murdering people, is it even worth going to that area at all?