First off, what is meant by the
OP's reference to commerce. Do you mean private sector commerce? Do you mean governmental level? For government level, see what previous posters have already written. The Imperium matches supply and demand for specialized worlds and deals in commodities, of which manpower is just one. There doesn't seem to be an Imperium-wide currency, though sector level currencies exist.
The Imperium does have noble houses, trading houses, and at least in the Calixis sector, corporations (that are structured more like a noble house than a corporation). These can and do engage in trade, however the time scale of contracts could very well be on the order of generations and start to resemble more feudal obligations than purely commercial transactions.
That there is extensive transport of materials is a given considering how hive worlds are described as being reliant on imports of food to stave off starvation.
For some glimpses of hive world society, try the
Necromunda rulebook. In it, the ruling house of the planet, has a monopoly on access to space.
To the greater universe Lord Helmawr is Necromunda and the planet is his to rule as he pleases. The patriarchs and merchant families of the Noble Houses vie for his attention, and are eager to perform whatever favours are necessary to secure landing and shipping rights, trade licences and tax concessions.
...
The Houses are manufacturers of goods of all kinds,from foodstuffs to armaments. These products are traded with the Noble Houses and in this way the wares of Necromunda reach the wide universe. A complex but efficient trading relationship has grown up based around the competition between the Houses to produce goods, and between the Noble Houses to buy them.
p. 62, Necromunda rulebook
So at least on Necromunda, the ruling house extracts wealth by charging for access to space, and presumably also via direct taxation since the head of the house is the Imperial Governor. In turn, the Noble Houses turn around and hand down contracts to the common manufacturing Houses. The products are then bought back by the Noble Houses either for internal consumption or export (via the aforementioned landing rights purchased from the ruling house). Imports (such as food) are presumably bought and then consumed directly by the Noble Houses or sold on for profit to the lower Houses.
In the Imperium, industrial capital is held by nobles or by governmental institutions. The Adeptus Mechanicus for example is described as granting Armageddon the license to manufacture goods like the Chimera. In return, the Adeptus Mechanicus probably would get either a cut of the production or some other payment in kind, such as other hive world products.
Individual shipping is described as basically falling under Chartist captains or full Rogue Traders. Rogue Traders are the true free agents since they are bound only by the limitations of their Charter. Chartist captains run standard routes, via charts instead of necessarily having a Navigator, and are thus restricted to the same set of cargo runs. Considering the monopoly on technology held by the Adeptus Mechanicus, and the costs of ship construction and maintenance, I would imagine multi-generational mortgages on ships (essentially debt bondage) would be the case, with them being in thrall to either nobles or other such entities.
Now if we turn our hands to the area of finance. The vagaries and time delay of warp travel prevent real-time markets on an interstellar level. Astropaths are also not depicted as so common as to be wasting their time sending messages about mundane information like equity pricing. Also individual worlds of the Imperium are independent from each other, aside from the veneer of overarching Imperial government and culture, so issues of trust in settling financial transactions can remain. Now banking did exist before quick communications, via the use of things like bank drafts, so think pre-modern banking in terms of various branches having to write cheques to each other. While not
40K, the GURPS Traveller supplement
Far Trader does an interesting bit on banking in a science fiction universe where travel and communication times are limited.
One key difference to also remember is the Imperium as a whole does not appear to be a consumption economy. Nobles may consume luxury goods imported from off-world, but the rest seem to either get by on local products or only on mandatory staple imports (such as food for hive worlds or
raw materials for forge worlds).