That's what I believe as well. If Vitani and Kovu were both Zira's offspring then they would have to be littermates because lion cubs grow fast and there would be a very easily distinguishable difference between their sizes if they were not in the same litter. And, since we know that Kovu is not Scar's son, and that Vitani and Kovu are in the same litter, we can say that their father was a rogue xD
As a fan, I like to believe that Scar and Zira were lovers, and that they were Nuka's parents. It's kind of difficult to believe that Nuka is indeed the son of Scar