Whatever feelings those may be, nebulous in spite of how generally understood they are, Shinji's still ready to welcome them and keep them nice and safe. He doesn't expect Kai to articulate all those feelings perfectly, and honestly, putting them them through with actions like the follow-up kiss are plenty to convey what he's feeling. Sometimes actions are just easier. More straightforward. Shinji understands.

This second kiss is still a little surprising, but doesn't quite catch him off-guard like the first one. He holds his breath for just a moment before closing his eyes and pressing forward, his hand leaving his chest in order to slide up to Kai's shoulder. This is good, the action seems to say as Kai's shoulder is given a gentle squeeze. Stay right here with him.