IL2 had wholesale changes to the way the flight model worked for many years after the initial release, as well as weapon strength and effectiveness. If something wasn't right they changed it, for better or worse sometimes. With Frontier.. we can have any thrusters we want.. but the ship goes the same speed anyway. It's just one example, but it reflects a lot of the design decisions made in the game.
Perhaps it was this way in some previous version, but this is currently not the case. Upgrading thrusters has a measurable effect on performance, all the way up to the most expensive thrusters a ship can take.