If you talk to Laguna and co on the Ragnarok before you go to the Lunatic Pandora, Kiros will say he has his mother's eyes, and that Ward thinks it's lucky he's nothing like his father. Another subtle clue that they know who Squall's father is, i.e. their closest friend, Laguna!

Otherwise, there's nothing obvious in the game, but I think it has been stated in the Ultimania guides in Japan that this is the case.