There's a multiple resource penalty for upgrading ships:
For example, you design and build a ship that requires 2 Thulium and 2 Promethion for its weapons. For the next iteration, you only change the engines and life support, but when you upgrade your existing ship, you have to re-pay the 2 Thulium and 2 Promethion again. That's 4 total Thulium and Promethion for the same weapon.
With resources typically so hard to find, upgrading ships hardly seems worth it. The upgrade mechanic is a remnant from before resources were required for ship components. I think it needs adjusting.