As I wrote somewhere, I believe none of Zira's cubs are Scar's, and that the reason why she's so loyal to him is because he allowed her small, wandering pride to stay in the Pridelands and promised to adopt her youngest and make him his heir. He basically only showed her his best face, isolating her from other lionesses and manipulating her into later thinking that Simba is evil and a murderer. Zira probably doesn't know too much about the crap Scar did, or if she does, she knows his version of the story.
When she was due to deliver her cubs, Scar sent her away to someplace safe, and told her pride to tag along to make sure nothing goes wrong, 'cause he was paranoid. When she came back, Scar was dead and Simba was the new king, leading her to piece things together the wrong way. Sha attacked Simba and he exiled her, her cubs being too young for separation.
So who's the real dad? In my headcanon, Zira's previous mate, who died or something.
Why does Nuka look like Scar? Well, since Kovu looks like Scar, and Vitani resembles Zira, the trio's dad might have looked somewhat similar to Scar.
Why didn't Scar even try to make his own heir? The lionesses from Mufasa's pride didn't like him and he didn't thrust them. By the time Zira came, he was either too old or simply didn't care.
Plus, I believe that, even if Scar didn't like Nuka, disownation would have been a bit too rough, even for him, especially since we are talking about a Disney movie.
But why Kovu and not Nuka? Well, even if in your theory Scar was Nuka's dad, my answer is the same. Scar had more intalligence then brute force, but does Nuka have either? From what we've seen of him, he isn't the brightest lion around, and it's his own stupidity and lack of planning that got him killed in the end. The chances of Simba accidentaly pushing one of the logs down towards Nuka was high on its own, but what did Nuka even want to do when he caught Simba? Have both of them roll down. The situation was quite risky and Scar wouldn't have put himself in it, in my opinion. Plus, Nuka had a lot of time alone with Kovu, so there were many things he could have done to get rid of him, even in a Disney movie. And it was also proven that if he was the chosen one, he would have blown the plan up by offing Kiara instead of Simba.
Sure, Scar could have taught Nuka to be smarter, but maybe, he just deemed him a lost case, which sounds a lot like Scar tbh. It was easier for him to start from scratch with Kovu, who just might turn out to be stronger physically too.
Also, the reason why Kovu was chosen over his older brother might even be more personal. Maybe Scar wanted to ridicule the traditional first-born rule that denied him the throne in the first place.
And as far as my theory goes, Scar, along with previously stated things, also wanted to be a full father figure to his new heir, while Nuka still remambered their real dad.
This all is, at the end, just how I see things. My personal head-canon a nothing more.