The civs will select ships flagged as colony ships and freighters during ship design. Ship designs always get flagged as something, even though that is currently hidden from the players. I guess it wouldn't do any harm to display that value somewhere.
A freighter (for example) is a design that does have cargo holds but doesn't have a GB engine, doesn't have a hangar, doesn't have a PPV above 0, doesn't have geo or grav sensors, doesn't have troop capacity, can't build jump gates, can't harvest or terraform, can't mine asteroids, can't carry passengers or colonists, can't salvage anything, can't maintain anything and doesn't have an orbital habitat.
Civs will pick non-obsolete, non-jump capable freighters with commercial engines that are within their budget and are more likely to pick popular types currently in service, weighted by percentage in service. If there aren't any service at the moment, they will choose the most expensive design they can afford with the same criteria.
When a shipping line is selected to build a ship it will choose freighters 50% of the time, colony ships 40% of the time and liners 10% of the time. If a suitable design isn't available, or too expensive, they pass on building anything.
Steve