One thing I haven't looked into was, do freighters cost ship maintenance? I'm just wondering if the mini-freighters are pouring more money down the drain then what they can bring in.
Yes, at least in DA freighters cost more than they brought in for the first 1-3 years depending on the map setting.
No, the mini freighters do not have maintenance costs - the initial freighter
does, but once it establishes the route it does not. I just double checked using the same startup game that I checked the maintenance cost of the starbase in.
This was something I initially complained about in DA, then I gave up and just stopped using freighters. Remember in addition to upkeep you have to figure in the initial cost of the freighter to figure out if you are making money. If the cost of freighters has increased at all (I haven't tested freighters in TA, I had just about forgotten they are a player option because they are so rarely cost effective). Plus any upkeep costs for economic starbases if you use trade modules, plus cost and upkeep costs of any military ships you use to defend your trade routes. If you can get any kind of reasonable return on a trade route vs. all of the costs in less than a year and a half you are a much better player than I.
Well, using the same figures from the test game I used to see what the maintenance of an econ starbase was (5bc/week), freighter maintenance was 7bc/week over 3 turns and econ base was 5bc over the same 3 turns. So the cost to set up my one trade route + 1 starbase with 10% trade bonus was 503bc (159/constructor, 149 for freighter - default ships, 36bc for upkeep until route was established).
The freighter was +1bc/week, so if it was by itself it would
eventually pay for itself

On the other hand, that 1 econ base + upgrade would much more quickly pay for itself if it were at a center for trade.
I almost always build an econ starbase that encompasses my home planet and the 2nd colony so that I could reasonably take that 503 and remove one constructor's cost making it only 344 (since I would have built it anyway).
So it can be profitable, but you have to make an effort to make it viable.
It does improve civ relations though, and that can be very, very helpful.