I just did some clinical test of this so we can all be sure how it works and it seem to work exactly as Steve said and intended.
Cargo Stations and Spaceports do NOT stack...
Cargo Bays stack, they even stack with the Cargo Stations and Spaceports. So a single Cargo Bay loading at a colony with a Cargo Station will load and unload twice as fast.
One effect is that ships with smaller cargo hold will be significantly more effective in terms of loading/unloading cargo while larger ships are cheaper and cost slightly less fuel to haul the same mass. Such as these two ships...
Adelaide class Cargo Ship 51,840 tons 227 Crew 803.6 BP TCS 1,037 TH 2,500 EM 0
2411 km/s Armour 1-123 Shields 0-0 HTK 61 Sensors 4/4/0/0 DCR 1 PPV 0
MSP 9 Max Repair 100.000 MSP
Cargo 25,000 Cargo Shuttle Multiplier 1
Squire Control Rating 1 BRG
Intended Deployment Time: 3 months
Commercial Ion Drive EP500.00 (5) Power 2500.0 Fuel Use 1.92% Signature 500.00 Explosion 4%
Fuel Capacity 250,000 Litres Range 45.2 billion km (217 days at full power)
EM Sensor EM0.4-4.4 (1) Sensitivity 4.4 Detect Sig Strength 1000: 16.6m km
Thermal Sensor TH0.4-4.4 (1) Sensitivity 4.4 Detect Sig Strength 1000: 16.6m km
This design is classed as a Commercial Vessel for maintenance purposes
Australia class Cargo Ship 257,247 tons 1,077 Crew 3,535.1 BP TCS 5,145 TH 12,500 EM 0
2429 km/s Armour 1-360 Shields 0-0 HTK 296 Sensors 4/4/0/0 DCR 1 PPV 0
MSP 8 Max Repair 200 MSP
Cargo 125,000 Cargo Shuttle Multiplier 5
Squire Control Rating 1 BRG
Intended Deployment Time: 3 months
Commercial Ion Drive EP500.00 (25) Power 12500.0 Fuel Use 1.92% Signature 500.00 Explosion 4%
Fuel Capacity 1,250,000 Litres Range 45.5 billion km (217 days at full power)
EM Sensor EM0.4-4.4 (1) Sensitivity 4.4 Detect Sig Strength 1000: 16.6m km
Thermal Sensor TH0.4-4.4 (1) Sensitivity 4.4 Detect Sig Strength 1000: 16.6m km
This design is classed as a Commercial Vessel for maintenance purposes
Five of the first ships will load roughly 40% faster than the second larger ship if a station is present. The reason is that each of the four smaller ships get assistance individually. But in general loading and unloading is still fast enough that I think the total cost involved for producing the ships is more important. In this case 3553 versus 4018 BP. You probably could throw in a few extra Cargo Shuttle bays in the larger ship to make the difference in loading marginal and still get a cheaper version of the larger one.
Important to note however is that adding cargo shuttle bays have a diminishing return and the speed reduction will often impact the rate at which you deliver goods, so be careful. If you make short trips, say deliver goods in Sol at the start of the game then loading times will be more important, when a round trip are more like a 6-12 months then speed is way more important. More speed also means that any installation you deliver will be inactive for less time.
Use large cargo ships for long runs and small cargo ships for shorter runs, that makes best use of either type. This also seem to fit very good with how I build my cargo ships... I usually have them in cargo sizes of 5000, 10.000, 25.000 and 125.000. I have 5000t mineral haulers that have no Cargo Bays at all, they rely solely on Cargo Stations and Spaceport and is only used to deliver minerals to colonies. I use 10.000t cargo ships with jump drives to support starting colonies with infrastructures, these are as fast as I can make them and I also have a matching colony ship type as well. 25.000t cargo ship are my mid size freighters that deliver most stuff at shorter distances one or two system max then the large 125kt cargo hold ships as the main work horse for long distance hauling.