This is a pretty interesting theory, one that I myself have switched between believing and not believing it. However I've settled with one: Zira was the Queen of Scar and this is why:



A scene, an scene from the Final movie, hints at the "deleted" scene called "Kovu's Bug" which can be viewed here http://www.youtube.com/watch?v=leiPvxuNop4 . Like "The Lion King" It takes place directly after the Royal cub's presentation and moves onto the villain.



Here Nuka and Vitani report to Zira, telling her Simba's new cub is a girl(note: New cub...Perhaps he had another cub before? Or it may be because Kiara is newborn cub so don't get carried away). Before this happens the scene firmly establishes, no Kovu was not Scar's son but yes he did chose the cub as the next King. Here Zira says it clear as day,



"Yes! Because of Simba! If weren't for him Scar would still be King. And I, Zira his loving devoted Queen"



Now I know what you all are thinking: It's just a deleted scene! That doesn't mean anything. It wasn't featured in the movie, so it's not canon.



Or is it?



When Kiara and Kovu stupidly wander into a mess of gators and escape, they begin to bond. Zira, who is hiding in the grass, looks at Kiara awfully hard, as if she's seen the cub before. She doesn't seem very pleased, which is weird considering how much of an opportunist she is. Kovu would need a queen or at least a mate to continue his line.



One might argue Zira wouldn't want to betrothe her son to a pridelander, which a seemingly sound argument. But it's pretty weak. It's not the Pridelanders Zira hates, as she used to be one herself and strives to be one again by taking over the Pridelands via Kovu. Sure she goes 'What have I told you about THEM?' but she never elaborates on who 'them' is. The Pridelanders? Or just Simba's family? The second one obviously.



The cubs go on to introduce themselves, and as soon as Zira hears Kiara's name, her hard stare turns into a snarl.



She obviously knows the cub, and that's she's Simba's daughter, the snarl proves that much. But how? Zira and Kiara really never interact until the movie's end...



The only way:



That scene was not deleted, but strongly hinted at due to time contraints. It makes sense. And then there's the fact every(or almost every. All the ones I have say so) SP book includes this scene.



Upon hearing Simba's cub is female Zira laughs, "A girl? Ha, ha, ha! Scar my beloved, did you hear that? This couldn't be more perfect!"



In my books Zira's response to the news is very much the same:



"There was news from the Pridelands-Simba's cub was a girl!"Perfect!"Zira exclaimed, "Girls will be girls, but boys will be Kings!"



and,



"Nuka and Vitani, Kovu's brother and sister, reported back from their secret trip to the Pridelands that Simba's new cub was a girl."



Heavily hinted at in the movie, said straight out in the books. It's basically canon if you ask me.



This scene is not exception. Almost all the deleted scenes are hinted at in the movie.

Nuka's original lasts words: He preps to say them(actually he does say "I") but Zira's shush's him before he can.(he actually gets the "didn't I?" part out)

Zira's suicide: Before Zira falls, Kiara's gives an extremely shocked look. Also, she can still be seen smiling before she hits the water.





Conclusion:There are a total of 5 deleted scenes in Simba's Pride. Two of them(Zira's suicide, Nuka's original death) were removed for content and the rest(Kovu's bug, The other cub, Nuka/Vitani's news) were not included due to time contrainsts. Vitani and Nuka's news was in the movie, though it wasn't actually visually there as it, unlike any other scene, is featured in books. Everything within that scene is canon as it is the only explination why Zira knows Kiara, none of the content contradicts anything the finished film says, and therefore comfirms Zira was Scar's Queen.