At the moment, a
ShaderMaterial can only affect an object on which it is applied. If you want the same material to be applied on more than one object, re-use the same material on them and it will affect them all individually.
modify the appearence of mutiple nodes as if they were one
Can you better explain what you mean by this?
As for modifying previously rendered objects alpha, this is not possible in the current API. What is drawn is drawn, you can only get the resulting pixel color on screen. There is no individual alpha information you can get from it. The only way would be to use a render-to-texture to compose into the final render, which can only be done with a
Viewport, which in turn might be quite overkill for a UI.
There might be a GPU driver feature to do what you want (at least maybe stencil buffer) but it's not exposed by the engine.