Because they weren't second cousins. We don't have any evidence that Scar is Zira's father. In fact, we have evidence in quite the contrary.

He wasn't Kovu's father, and he isn't even confirmed to be Nuka and Vitani's father, so just as well there might have been other males around before Zira came into the world - which by the way I would think was around the same time as Scar and Mufasa. To me, she seemed around Scar's age in the film.

Beside's Zira calls him Scar and not father & talks about him in a very non-child/parent manner.

Not really, apparently Kovu origionally was supposed to be Scar's son, but Kiara and Kovu would have to come together so they changed it, even though I do think that Kovu looks too much like Scar. And like bendaimmortal said it hasn't been confirmed that Nuka and Vitani are Scar's, but it would explain a little why Nuka has such a passionate hate for Kovu being "The Chosen One" when it could have been his birth-right.

Yeah, and it's been said that Nala's father was either Scar or Mufasa, making Simba and Nala related either way. But they're animals, I don't see why everyone is flipping out about it.

heres a family tree of all the lions ever stated in both books & movies to help make a clear picture :)

well as it turns out that i found that ziras perants are lulu and kalsifur.....mufasa and Taka (scar) are brothers other then that no relation between mufasa and zira...vitani and kovu both are from zira and cole well nuka is from taka (scar) and zira...witch means that kiara and kovu have no relations....nuka dint like kovu because with out simba and taka (scar) there blood line would have been nuka but kovu was the "chosen one".....nalas perants saratina and shaako...so the first question no they are not all related

I don't think Scar is Zira's father, I think Scar and Zira are mates and I think their children are Nuka and Vitani (I think Kovu is adopted). That's my theory.