I'm probably the odd one, but I actually believe all of them are Zira's, and none are Scar's. Mainly because I saw someone who took part in the making of TLK2 discuss it, and that person said that they never really saw Scar as the father of the cubs - I'll try to find that somewhere. I know they've been his in the early productions, but they might have dropped that because of the Kovu controversy, and Disney keeping their 'normal family' ideals.
Still, since nothing was really mentioned in the movie itself, I guess it's up for interpretation. Here how I see things, and some things in canon that go along with my theory. Of course, this is only my fan canon, and nothing more.
I believe Zira lead her small wandering pride of lionesses in the Pridelands during Scar's rule. She was pregnant at the time, had a small cub Nuka, and has recently lost her mate. Scar, who was in mad need of a loyal heir, promised to give them all a home if she allowed him to adopt and name one of her unborn cubs the future king, preferably male. Why didn't he have a cub himself? Well, we know lionesses in the pride probably didn't really fancy Scar, so even if they gave him a cub, they would probably actively try to raise that cub their own way. Svar couldn't separate the cub from their mother until it was too late for him to corrupt it, and he knew this. He also knew that he wasn't the strongest lion out there, and that his own cubs would have to rely on hyenas for brute strength just as much as he does. But, if the cub Zira bore him was strong, and if he had a chance to raise him along with Zira, who'd be loyal to him... it wouldn't make all that much difference. In order to make Zira his pawn, he only showed her his best face, and isolated her from other lionesses who might have told her anything different. With Zira, she probably only saw Scar as the kindly king in a really sad situation, who relied on his own intelligence rather then strength.
Moving on. Zira's time to give birth comes, and Scar sends her away along with her pride members, somewhere that's secluded and safe, because he's paranoid that something might happen to his heir.
At that time, since there is no Zira's pride to haunt for him, he calls out for Sarabi and they argue. He hits her, Simba comes, kicks Scar's furry butt... yetta yetta.
When Zira comes back with Kovu and Vitani, she attacks Simba, and Simba threatens to exile her. Kiara is born at that point. Zira does something bad, like attacking Simba again or... I dunno - and Simba, angry, exiles her for good, along with her pride and all the cubs, who are too young to be separated or make a choice on their own. To give some canon proof. Zira said that Scar adopted
her son Kovu and announced him as the future king, and that Kovu was born last before Simba exiled him. If both she and Scar adopted Kovu - wouldn't it make more sense to say that
they adopted him.
Sure, you can say Zira is delusional in some aspects and shouldn't be trusted, but I believe if that was the case, Disney would directly point that out, just like they pointed out Kovu not being Scar's son. Besides, I for once don't think Zira was delusional in any way - she looked more like she had serious anger problems, and probably didn't know about Scar's wrongdoings completely. She doesn't only want the throne, but she also wants vengeance. For what? Scar was murdered and her pride was exiled. Does that mean Zira views murder as a crime worth avenging, eye for an eye? Think about it, she does attack Kovu about having had killed his own brother, and calls Simba a murderer- that means that both things don't go along with Zira's morals. If she knew what Scar has done... would it be logical for her to act this way? This would actually explain her angry and vengeful behavior rather well- she believes her side was wronged. She confirms this when Nuka dies, as she says that Simba has
wronged her for the last time. Simba is the bad guy from her perspective, and has to pay with his life, and she also feels responsible to carry that out because Scar named her son his heir. On the other hand, if she knew Scar did horrible things to get to the throne, and if she supported that - her anger would look differently. She wouldn't claim Simba was the bad lion, and there would be no need for revange, but she would still actively try to get the throne.
Then there's Nuka who says the same thing. Scar wasn't Kovu's father,
he just took him in. Scar took him in, not Zira. If Zira wasn't Kovu's mother, why wouldn't Nuka say that
they took him in? Or if Zira found the cubs in the Outlands, why didn't he say
she took him in? Nuka would definitely be the one to have this knowledge, because he was a cub at that point, and didn't get separated from Zira - he'd known if she got pregnant. Sure, you can call Nuka delusional too... but that would suck if everyone just happened to be delusional.
Another important point. Nuka never refers to Scar as his dad, either - not here, not in the cut scene, not anywhere in the movie. He always refers to him just as Scar. Nuka also never gets too emotional regarding the lion - he mostly cares about impressing Zira and having her appoint him as the chosen one. That means he never considered Scar a face of authority for him. Same goes for Vitani. And when Nuka dies, Zira asks Scar to take care of
her little Nuka for her. One might say that Nuka looks like Scar... but so does Kovu. They might both be sons of some dark-maned, dark-furred lion, and Vitani could have inherited her mother's lighter fur. As for her blue eyes - genetics.
And last, there's Disney's family values. They are going to be very careful when depicting a family - cheating and having multiple mates is usually a bad idea. But if none of the cubs were Scar's, that wouldn't be a problem - he just appointed the one he liked the best as his heir.