I don't know about all that warehousing business. A free trader's not going to worry about warehousing - the cargo owner will be doing that while he's seeking someone to carry his cargo. And, since the ship is the biggest cost, one presumes a scheduled liner like Tukera will make whatever warehousing provisions are needed to keep their ships moving at the most efficient rate. I'm thinking loading and servicing the ship is going to be the main time factor.
Real world is not a great analog for far future game circumstances, but it's the best we have:
I see an example of a cargo ship being loaded with 7200 long tons in three days. In that case, there are 5 crews with equipment loading through 5 hatches. A standard 30-ton shipping container can be anything from 4 to 8 dTons, so figure that's maybe 240 containers, 1000 to 2000 dTons in Traveller terms. I'm not sure it's all containerized, but it's a RoRo, so it loads and unloads like a Trav ship would - or at least more so than the big ones that strap so much to their decks.
The typical Free Trader carries quite a bit less but isn't blessed with 5 hatches. No reason it can't use shipping containers, but best use of space will probably involve taking smaller packages as well. Still, one should be able to load it in a bit over a day, 3 to 4 8-hour shifts. Unloading, maybe same. So, assuming roughly similar techniques, you ought to be able to unload and then load in 2 to 3 days. Far future may bring some improvements in loading equipment, but I don't envision radical improvements in loading speed. One presumes your ship can be fueling and your systems receiving needed maintenance while all that is going on.
This assumes a hired crew of longshoremen (or robotic equivalents) with equipment, which isn't actually mentioned in canon, and I don't think the Cr100 docking fee is enough to cover that. I'm guessing
very roughly that hiring a crew and their equipment could set you back as much as Cr500 - 1000 for the whole job (so figure it roughly at Cr5-10 per dTon, just to make it easy to figure). If you save money by doing it yourself with your crew, you aren't going to be able to manage back-to-back shifts, so - assuming your crew's about the same size as a typical loading team and that the Cr100 docking fee does give you rights to some loading equipment - 2 to 3 days can become 6 or more, maybe a bit less if you can manage 10 or 12 hour workdays (you slave-driver:devil

.
That is of course a very rough estimate based on only one example.