Kazuya suspected it for a long time that the original person meant for this mission was Rhys. Even before they arrived in the Mist Kingdom, Rhys displayed such signs before. At some point in their friendship, Rhys often disappeared, and when Kazuya saw him, he seemed to be busy working on something. When Kazuya inquired or rather once he tried to take a peek at the work, Rhys was doing. Rhys quickly found him and told him that this wasn't for kids. He didn't like how Rhys treated him like a child; there's hardly an age difference between them after all.
The events of earlier further confirmed his suspicions, though Rhys is pretty much like that towards any girl. He slipped up. Kazuya noticed something different when his friend spoke to Lyn. Yes, it wasn't the kiss that gave him away.