Several of the Shaman's abilities (including Fire Nimbus, Stardust, and Sparking Aura) indicate that the target gives off some amount of light "preventing it from gaining any benefit from concealment or invisibility". Does that mean that if the target is in the area of effect of Deeper Darkness that other creatures can still see it normally and attack it normally?
I compared it to the language in Faerie Fire, but that spell very clearly does not override the effects of Deeper Darkness, whereas the Shaman's supernatural abilities might. I can find nothing relating these abilities to comparative spell levels, as the hierarchy of Light and Darkness spells would require.
If it says that you can not benefit from concealment or invisibility that is pretty cut and dry, and it can be attacked normally. I have not read those abilities. I am just going by what you typed.