When you create a material in Maya, it exists across all Render Layers. If you create multiple layers with objects that use the same material, they’re all referencing the same material node. Therefore, if you adjust any parameters on that node, they will update across all layers.
If you wish to make layer-specific adjustments, you need to first right-click a parameter and then choose “Create Layer Override”. It will mark the parameter orange, which indicates that any change made to it will only affect the current layer.
You can override the same parameter on different layers, to have different settings. Parameters that are not overridden, will inherit their settings from the master layer.
Deleting the material node will delete it from the scene, and therefore from every layer. If you wish to “remove” the material from a specific layer, you should simply assign a different material to the object in that layer.