Though you have a point. Why not send supplies up in extension modules or interplanetary starship parts?
I believe that was the technique the Russians used on Mir, where each module had its own engines and docking hardware, but that means you end up with a lot of useless engines and fuel tanks and you lose cargo space because you have to ensure that people can live inside it for years. Plus you need to put a docking port on the back of each module to replace the one it's docked to, so there's less cargo space.
So it's not a bad idea, but it's not an obviously great one either.
As for the shuttle dropping off garbage, I believe they have to close the payload bay doors before firing the engines to reenter, so that's not really workable either. If you try reentry with the payload bay doors open because they didn't close after you dropped off your garbage bag, then you die; if they don't close before the reentry burn they can send an astronaut out to close them manually, but there's not much time afterwards.