It would help if we knew what was being stored in the cargo spaces of Trek spacecraft.
Basically, we get to visit starship cargo holds in ENT, DSC, TNG and VOY, in in-universe chronological order. (In addition, DS9 features cargo processing spaces, but of a somewhat different nature.) In most of those cases, we learn of no A-to-B moving of cargo - but we don't exactly learn of the contents being supplies, either, that is, ship's stores needed while underway.
The TNG bays generally appear to lack an "outer" door altogether, and probably are supposed to be ship's stores, locations for keeping spares or emergency rations or research team instruments or whatnot. Distribution would be via internal transporter or manhandling of containers (which generally appear to be ideally sized for both roles, being the size of a man and therefore both transporter-compatible and "spatially manageable", once one slaps an antigrav onto them). No doubt even a replicator-equipped ship would have plenty of need for supplies stowed in blue plastic barrels or fancily shaped boxes.
A couple of TNG bays plus many VOY ones do have outer doors, that is, ones opening directly to space (and never mind that these ships don't exactly have vertical outer walls that would provide for such doors and for an unobstructed starscape beyond). Arcane stevedoring methods would be available, then, no doubt involving extensive use of those pretty little workbees.
On occasion, the E-D does haul stuff from A to B, though, such as in "The Child": a priority shipment, carefully packaged as general goods rather than bulk, but in some quantity. Might be the ship's stores type holds suffice for that. Might be the ship has separate holds for the purpose. Heaven knows she has enough interior volume for that, and for a couple of small towns or indoors mountain ranges for that matter!
But we know dedicated ships haul cargo in Trek, too. And almost invariably these use container-type holds, but almost as invariably the containers are of a ship-specific, non-interchangeable type. Which is probably for the better: the logistics of tare management can be omitted when these containers only move when attached to the ships, or when being moved to and from a loading terminal of some sort at the spaceport. That is, there's no distributing of them from the big ships to smaller barges or road or air transport, or extensive storing at container parks, or anything like that. Containers today move best between peer ports; Trek ports would be the epitome of inequality, with capital worlds shipping stuff to one-horse colonies and vice versa.
It's a bit curious that we never see true bulk transport after ENT. We do hear of "ore" being hauled, but the one or two times we actually see it happening, the ships involved are minuscule. Okay, so perhaps "ore" is a bit of a misnomer, and the product is in fact highly refined already, but still...
What else? We know basically nothing about interstellar economy: do goods move from planet to planet solely in emergencies and during construction projects, all movement ceasing when a planet gets self-sufficient? After all, planets do appear utterly isolated, e.g. Deneva remaining silent for a year before anybody pays any attention. Or is, say, ore or grain being regularly shipped? Turning planets into breadbaskets with the Genesis Device would appear futile if grain can't then move across space to those places in need (they themselves can't be bombarded with Genesis, obviously). But we never hear of grain moving: even in TAS "More Tribbles", what is being moved in the robotic ships is special stock for eugenics purposes, not bulk for consumption.
Curiously, many cargo ships appear to be superfast: the Xepolites make a living on that, but Kasidy Yates also does circuits through multiple star systems in a matter of hours. Is this exclusive to tramps, or do packets and other regular services also operate that way? Why is "a freighter's speed" apparently universally just warp 2 in "Friday's Child"?
Perhaps we're missing big pieces of this puzzle yet, and a lumbering bulk carrier will finally be spotted in some future spinoff...
Timo Saloniemi