Ah, the old question of "what is a tonne of cargo, anyway". Been discussed in numerous old threads that I can recall.
The best answer, consistent with both the lore, and what we actually physically observe:
A standard cargo canister is roughly 1 metre by 2 metres. A standard cargo canister also weighs exactly one tonne. This also means that "1 tonne" of any given cargo is actually going to be less than 1 tonne net weight of goods, depending on what kind of packaging is going to be required.
1 tonne of bauxite doesn't need much protection from the elements, but neither does it need 2 whole cubic metres of space. So it's going too be packed with plenty of air. Assuming the cargo container itself weighs about 50 kilograms, this would give you 950 kg of actual bauxite in the 1 tonne canister.
1 tonne of perishables (fruit, meat, etc) is going to be considerably less than 1 actual tonne, because it will need climate control (refrigeration/heating) and probably pressurization (lest the cargo explode in vacuum). So, maybe 800 kg of perishables, and 200 kg of containment.
1 tonne of gold requires much much less than the allocated 2 cubic metres of volume. I imagine it sitting as a small cube of gold enmeshed in the middle of the canister, surrounded by beams of aerogel locking it in place so it doesn't rattle around inside. So again, about 950 kg of actual gold, and 50 kg of packaging.
1 tonne of hydrogen will need to be pressurized/liquefied, and no amount of magical hyperscience can shrink the physical requirements here. So maybe 750 kg of actual hydrogen and 250 kg of containment.
It is well established in lore that 1 tonne of slaves equals 1 slave. So that 1 tonne canister of slaves contains just one slave (80 to 100 kg), plus whatever life support is needed to keep them alive and healthy during transport.
It all sounds very inefficient - basically, wasting valuable space on board a starship shipping a bunch of boxes of mostly-empty-air around the galaxy, volume that could have been used to, I don't know, pack in some more cargo. But the critical factor of spaceships in ED is weight, not volume. And spaceship manoeuvring computers need to know the weight distribution within the cargo hold accurately. So a universal standard cargo system was invented and employed galaxy-wide, guaranteeing total weight of a canister to be precisely 1 tonne.
Of course, all this leaves unanswered the question of where all this mass to create empty cargo canisters in a refinery rig comes from - the hyperscience of converting milligrams of mats (iron etc) into the kilograms of structural material needed to make a cargo canister. Not to mention turning miligrams of mats into an entire tonne when you make a limpet.