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Elunite Ore is a quest object for the Alliance Warrior quest The Shade of Elura. The ore can't be used by Miners or Blacksmiths for any of their crafted items.
Source
Elunite Ore can be found in crates around a shipwreck near the Auberdine lighthouse in Darkshore.
Notes
To find the shipwreck, go to the end of the dock near the lighthouse and then head south through the water. You should eventually see the shipwreck.