So, having tested this further, my earlier advice appears to be largely nonsense.
Only the 1st cargo run seems to go from the outpost you spawn at. So if you want to load up on them you will need to do a bit of sailing around.
You can still load up on crates for normal MA missions, cancel, then drop some cargo runs, collect the goods from the outpost, get the animals on the way and just keep dropping new cargo runs or animal missions while you are out at sea.
Coming around to the OPs POV though, the rewards are much lower than I thought for the time invested. If you complete them in conjunction with other voyages they do become a nice little side earner.
I enjoy that they are relatively short and normally don't involve too much running around. Overall I think they are a good addition, but I think it's best to think of them as a part-time job on the side rather than a full-time career.
1x MA and 4x Cargo runs did earn me around 20k but we're talking more like 3.5 hours than 1.5 hours. So it's not great money for the time when you consider some of the other money making options available. It is a relaxing and entertaining way of earning a bit of MA rep and gold though.
Don't worry too much about running out of time either, that's a funny one, the label falls off and it just tells you "Good luck" but so long as you remember who's getting what you seem to still get full price for the goods so long as they are in good condition.