Ok, I know I said that commersial ships was uninteresting but I did some investigating into different engine to weight ratio on freighters.
I use Ion technology engines and two settings, x0.5 and x0.3 power settings... The freighters carry one standard cargo module, that is 25000 ton cargo capacity and all engines are 50HS engines, no point using smaller engines than that on larger commercial ships. All the ships use a 250.000 litre tank module and one cargo handling module. In reality you might optimise the design more these are just for a good reference point.
On the .5 power setting I get the following values
FI=Fuel Index, which mean how efficient it burns fuel (for cargo mass carried) in comparison with the other ships, higher is better.
CI=How efficient the ship carry cargo in relation to its build cost and speed, higher is better.
A: 10xEngines, 2900km/s, 1050BP, 56FI, 69CI, 51.100t
B: 5xEngines, 1940km/s, 617BP, 75FI, 78CI, 38.700t
C: 2xEngines, 967km/s, 358BP, 94FI, 68CI, 31.000t
For the .3 power setting I get...
A: 12xEngines, 1911km/s, 612BP, 180FI, 78CI, 56.500t
B: 4xEngines, 997km/s, 3287BP, 280FI, 75CI, 36.100t
C: 2xEngines, 580km/s, 255BP, 340FI, 57CI, 31.000t
My finding is that for Ion tech engines you should have about 2000km/s speed on your freighter for long range delivery to maximize cargo carrying efficiency but slower 1000km/s on shorter trips. The reason is that we do not include load/offload time in these calculations and in shorter trips such as delivery within the same system loading and offloading will take a considerable time of a ships time spent rather than travel. Also, slower ships will save a considerable amount of fuel, so building ships slower will only lower the cargo efficiency in a minor way sometimes not at all but will save you fuel, you just have to build more of them.
There are generally not a problem building many freighters since they build so quickly anyway, especially of you divert a small percentage of industry to construct their engines in advance if time is important to you.
Although, the cargo efficiency between these two engine types pretty much remains the same, using another engine just reduce your fuel usage, more or less.
You can't apply this on, say cryo ships, because cryo modules are MUCH more expensive than cargo modules. They require a completely different strategic approach to designing an efficient ship.