Civilian commercial shipping is built entirely independently from your Imperial shipbuilding capacity. It is my understanding that there are essentially invisible Civilian shipyards which are considered to be responsible for all purely Civilian construction. These shipyards start out at the standard size for a new Commercial Yard, and must be expanded to an appropriate size before laying down new construction. This is one of the reasons Civilian Shipping Lines appear to be spending money without producing ships. A commonly used strategy is to design a freighter around a specific cargo capacity. Generally, the standard cargo capacity is 5 Cargo Holds. Having 5 cargo holds allows an individual freighter to haul an entire installation of normal size, which prevents unfortunate problems with rounding errors. I have experienced this particular problem myself, and found it rather vexing. Larger freighter designs generally contain integer multiples of 5 Cargo Holds, for the same reasons.
As a side note, I prefer to design a freighter with 5 Cargo Holds, and some arbitrary speed in mind, such as 5000 kilometers per second. As the March of Progress continues onwards, I can design a lighter ship with the same capabilities, which allows existing shipping lines to produce new ships even more quickly. Holding some arbitrary, but high, speed in the design also means that even older designs will serve your purposes perfectly well. And never forget, that researching Power Gains at the expense of Fuel Efficiency can prove marvelous when designing a purely Civilian freighter. After all, Civilian ships don't consume fuel.
