From my experience with 3D game development, showing/hiding pieces when necessary is a common way to do it. You could also combine this with a spawning/destroying system if you want, so invisible clothing and armor is destroyed when unequipped. That way, you don't have a bunch of hidden nodes in doing nothing 90% of the time.
Though, I have not tried to make a interchangeable clothing or armor system in Godot myself, in 3D or 2D, so I'm not sure if there are better ways to handle this in Godot.