Old engineering saying: A perfect machine has the fewest parts to do it's job. Or, build ships big enough to hold it's mission components, and no larger.
When I build a cargo ship at the start of the game, I usually put 1 standard cargo component (the mission critical device), enough engines for about 450 km/s (good enough for the inner system), 1 cargo system (because 10 days to 2 days is a massive drop), and enough fuel for ~4-10 billion km (mostly so I don't have to micro the cargo ships). The entire design revolves around the cargo component, and is 'almost' the most cost effective design you can make for short distance transport.
If I want to move to a further destination, then a faster ship is preferred with bigger/more engines, even larger cargo holds and less emphasis is put on cargo transfer rate.
Military ships are similar, although the mission critical components are the weapons. EG: Missile ships need enough missiles to bypass the enemies' PD and do damage, enough fire control range to target the enemy with multiple salvos, enough defenses to repel the counter-fire, etc, etc.