The reason you won't see many box ships is because designing a ship will take time, and due to its complication, there's no reason to just do a poor job of it and build a box. You might as well - if you're not going to put the effort into it - just buy someone else's pre-designed ship that is really good for the purpose you want. The downfall of the box design is that it is good all-around, but not better at any one thing.
I would say, you will see lots of box ships early on, as people want to build ships that "do it all" - if you look back to the first cars ever made, they were very boxy for example. This will be true in Starbase, the early ships will be boxes because players won't know what kind of thing they want to do best, and don't know how to best achieve their goals, so a generalist box-ship is the best option early on, as it affords the player the most flexibility. Over time, the trend will be away from this basic shape, towards more purpose-driven designs.
I think arguing either side of the point is correct, however only the time frame changes who is 'right'. I would stand on the argument side which states long-term meta will almost never see box ships, as more refined designs will be faster, more armored where it's needed, and provide only the functions those ship designs need. Seeing a box ship after a few months will be like seeing an easy kill, or an unimportant competitor in the marketplace. Like an oil baron seeing someone hauling propane containers in his pickup truck. Or a Ford Model-T compared to a Formula 1 race car. There will barely be any comparison.