Maya creates certain nodes at the creation of a scene that it uses as defaults. I'm not sure why you can't delete them I'm guessing because maya uses them as a fall back in case something goes wrong or missing.
For example "lambert1" "particleCloud1" and "shaderGlow1" are nodes that can't be deleted because certain shaders use them (particleCloud1 and shaderGlow1" or because maya assigns them to every new object (lambert1).
I'm gonna guess "effects" is used by (for example) paintEffects and deleting that node would cause errors when trying to use paintEffects.
In an empty scene, there is always a non deletable default layer, that ist invisible in the layer editor (but not in the Outliner). I have the same problem with fbx and max. I think fbx renames the default layer to "effects" Have you tried to remove everything from the layer and rename it to defaultLayer and see what happens?
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For example "lambert1" "particleCloud1" and "shaderGlow1" are nodes that can't be deleted because certain shaders use them (particleCloud1 and shaderGlow1" or because maya assigns them to every new object (lambert1).
I'm gonna guess "effects" is used by (for example) paintEffects and deleting that node would cause errors when trying to use paintEffects.
Its quite a coincidence that, it was me that actually called the layer 'effects' but i get what your saying about having non-deletable nodes.
I also happen to notice that if i try to rename/change color or display, its just stuck on what it currently is and wont change. Possible bug?