The main reason not to use the noob ships for this purpose is their FTL tanks are really bad. If you have planets that are far out, having a speedy ship that can actually hold enough fuel to go to the middle of nowhere and back at max FTL can be quite useful. Of course if we can upgrade them, it would definitely make the smaller cargo bays even less useful then they already are since we could slap a larger ftl fuel tank on a noob ship.
I agree, for the total cost of the ship being fixed for a lot of components, it doesn’t make sense. I think what really needs to happen is more granularity in ship components, especially BR and CQ, and have the smaller ships be significantly cheaper or, more importantly, lower tech.
Another balance change that would help make the smaller cargo bays useful is if we would need multiple (much cheaper) STL engines on a ship depending on the size of the cargo bay. In real life, the more mass your ship has, the more thrust it will require if it is going to reach orbit. For an example of how this could work in game, the number of engines required could be 1 for a ship with a tiny cargo bay, 5 for a large cargo bay, and 8 for a high load cargo bay.
To balance we would need to remove the ACS from the STL engine formula (especially since the description of this item specifically mentions FTL reactors), and each engine would require 1 Fuel Pump, 1 Nozzle, 1 Flow control device, some Fluid Piping, some quantity of Thermofluid (coolant) depending on the type of engine, an amount of metal or alloy of an appropriate level for the engine, and a fastener kit.