Ah, no. Darknuts were definitely not only seen by Link. You find several of them frozen within Hyrule Castle in Wind Waker-- thus Ganondorf obviously was in the habit of using them in his take over. He likely did so during Ocarina of Time although we never see them. Besides- he's 81/2 feet tall. That's inhumanly large. S'gonna freak people out whether they know exactly what a darknut is or not. Unless he tries to play it all off as a crazy costume. 

As for the light arrow-- while it was imbued with light it was also an arrow. So of course it could still harm other things. It's the light itself that kills dark creatures so quickly. You can't deny that they were at least followers of Ganondorf for a time. I'm not going to push that they were created by Ganondorf, but judging by how Iron Knuckle came to be and the fact that they are dogs, I've just always preferred to believe Ganondorf bred Dauchsons and turned them into Darknuts-- manipulating their dog-like loyalty for his own evil purpose. But that's just speculation-- no more canon that HTW.

With the Zuna, you have to keep in mind that I'm going strictly off the Wiki and [i]not[/i] Hyrule Total War. (I'm not much of a war RP kinda gal and this is far from a war-like RP.) But either way-- only Gerudo would likely know of them. 

I don't mind if you want to base the Darknuts off of HTW. I understand that the game leaves many things unexplained and I'm pretty flexible. Really all I'm asking is that the city be outside of Hyrule. Something like what Lug suggested would be just fine and I doubt it would affect much for Captain E's background. 

As for the whisper-- yeah... pretty sure it's obvious enough. Glad you caught that.

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Lug, I'm glad you liked it! Thought you would. :D Them boys are all yours. Do with them what you will. (Their names are Rigby and Mordecai by the way. Otherwise known as Mordecai and Rigby. Otherwise know as a totally shameless rip off of The Regular Show.)