Hmm. Given the circumstances under which they met, if there was anything there it was extremely minor - by the time they were reunited in the desert arc, he was well into the "lol Fllay" side of things. So if he did have any attraction to her, it was probably buried under "Fllay" and "busy, gotta protect the Archangel." And then there was Lacus. And then he learned she was his twin sister.

I actually kind of... it's weird, and it's been so long since I've seen original SEED that I could actually be factually wrong about this, but I always got the sense that Kira had a sense that the Yamatos weren't his actual parents. They were Naturals, and while they COULD have just gotten their child turned into a Coordinator in utero like so many others, it's definitely something that probably came up in his mind - and he didn't really look like them, either.

Even with that in mind, I don't think that learning they weren't his biological parents would have been that much of a shakeup to him (at least, not as much as learning what he actually was in the laboratory with Mwu/Rau). He still considers them his parents whether they're biological or not, because he's all about believing that the genes you have are only a part of who you are.