Hi monsterzero!
Stations and ships are scaled with the faction strength, so the closer you get to the center of the galaxy the bigger they will be. This has the following nice effect: after playing for some time when you return to some earlier, weaker sector you're really overpowered ;D
It really shows the progress you've made!
If you build a ship that's too big you need more crew, money, energy and thrust, so you can't just build infinitely big; it's limited in a natural way. On the other hand if you can you've earned it.
Concerning docks:
Docks that you can fly into are no good when your ship is too big. I think the current solution works well; you don't need to touch it but you need to be quite close, so if you want to dock often, you better have an agile ship ;)
In the full version docks have a distinguishable "dock block". If it gets destroyed it's gone.