True, thats ok for certain effect shaders.
They are a nice optional addition.

I am talking more about shaders that dominate a certain scene.
Take the bloom for example. When using bloom, you need to change
the brigness and lightning of the textures in your game to make it all fit together.
Now if the player switches off the bloom, it will look really ugly and inconsistant,
as the scene is too dark and has a strange contrast.
So I would have to eveluate, what brings the bloom to enhance the athmosphere, at what costs (FPS).

Other is the usage of dynamic shadow casting shaders.
They are used even if the gameplay does not require a dynamcical shadow world
in the end. And they really drain performance. (thief 3 as a bad example)
Now if the player needs to turn it off, the game will look really ugly, as
the whole shadow part is gone, that gave the scene the needed contrast.