I'm not sure how that'd interact with your rework on them, so it's all from VB, I'll admit.
Can you make it so a planet that isn't visited regularly by civilian colony ships slowly becomes more and more attractive to them?
Often when I have one homeworld and say 2 colonies at col cost 0, civilian colony ships will only fly between the homeworld and the closest colony, unless I set it to "stable" for some time. (I suspect even with your change, civilians colony ships would only fly the route that gives them the most wealth/time and forget the rest exists.) So could you make it so if the second, more distant colony hasn't seen civilian colony ships in a while, the reward for civilian colony ships would slowly ramps up until eventually they find it more interesting than the closest colony? It'd slowly go back down as colonists start being unloaded there.
I think it'd be better to make un-flown routes offer more money than make the over-used ones offer less, it'd keep their and your income about constant. You'll likely get a bit more since between the time they decide on their new target that'd bring them just one more wealth and by the time they get there, the reward would have kept going up. If you make their most-used routes less rewarding though they'll go use another, make it less rewarding and keep switching, making all the trade routes less and less rewarding, spiraling down until they're not making any money anymore at all. If there's a hard cap to ensure there's always a decent-ish minimum reward, some routes would still appear less interesting than another's minimum and never be used at all.
I'm not super sure it affects freighters because I only ever get very few of them, but it seems having more trade goods to pick from than just "colonists" helps them fly more randomly and that they might not need incentives to fly to other places.