In practice, what matters for commercial ships is not size, speed, etc. but
effective throughput. This means you need to factor in build cost, fuel usage, etc.
Consider a freighter with 25,000 tons cargo space and attendant necessities, let's say it costs 250 BP for all of this. Suppose I can put 25% of the total size as engines at whatever tech level, costing another 250 BP and a speed of 1,000 km/s for sake of example. Now say I double the engine size, costing yet another 250 BP, and I can achieve a speed of 1,600 km/s as my engines are now 40% of total size.
So for 500 BP I can get a freighter that moves 25,000 tons of cargo at 1000 km/s, or for 750 BP I can get a freighter that moves 25,000 tons of cargo at 1600 km/s. If you assess the throughput per BP you will see that the latter freighter is a bit more efficient for the cost, so far this supports the argument for a larger engine fraction. However, there are several complications:
- Engines cost gallicite, and gallicite is often a precious resource and highly valuable. Not all minerals are created equally.
- This math depends on engine cost relative to the cost of everything else - cargo bays, shuttle bays, etc. don't change in cost over time but engines do. If your engine block costs you 500 BP for 25% of the total mass instead of 250 BP, the above math will work out (slightly) in favor of the first freighter. Therefore it depends on your tech level.
- We also have the opportunity to build a bigger freighter in terms of cargo space rather than engines. Suppose it would cost us 100 BP to double the cargo space in the example above. For 750 BP I could get a freighter moving 25,000 tons of cargo at 1600 km/s, or for 600 BP I could move 50,000 tons of cargo at approximately 570 km/s. In that case, the faster freighter is still a bit more efficient. However, if the baseline engine block costs 500 BP instead of 250, the higher-capacity design starts to pull ahead - but again, the difference is not very large.
In many cases which are of practical relevance, the difference in throughput efficiency (per build point) is not very great, perhaps a 10% difference between different options. When you get to higher tech levels with high engine powers and small minimum EP modifiers, then the analysis can shake out that certain approaches will be much better than others at least on paper. For example, the effect of the EP modifier on engine cost when it is below 100% is (EP modifier)^2, which means a 40% Ion Engine is going to be cheaper than a 50% NGC Engine of the same total engine power. I did not analyze the EP modifier effect above but it becomes very important.
Add to this, you will have strategic and operational concerns beyond pure economic efficiency, for example a freighter with 10% efficiency engines might be the most cost-effective, but if you need to deliver 10 million people to a system 6 transits away to establish a naval base before the aliens come then such a slow freighter will not be suitable for the task. Consider also the value of building multiple ship classes from a single shipyard; the math looks very different for a colony ship, since cryogenic modules cost an order of magnitude more than cargo bays for the same tonnage. In a vacuum, a faster colony ship is quite likely to be the most efficient design, but that means your freighter class must be much more expensive if you want to build it from the same yard.
So the tl;dr version is this: there are a wide range of commercial ship designs which are viable and arguably optimal under different conditions. In practice, you will probably have far more pressing considerations than getting the most efficient possible freighter, colony ship, etc. My advice is to prefer what is simple and easy, because it will work well enough for your needs, and then look into making changes as the situation evolves in-game. In Aurora there is rarely a true optimum so why worry about finding it?