>>4082939The latter, probably. When Shinji notices Asuka he's visibly shocked. And his movements weren't like they were in the kitchen scene; we've all seen that Shinji gets uncharacteristically volatile when he's angry, and this wasn't that. It was more like a trauma victim moving on autopilot.
With the hair covering his eyes, I saw it as him already resigning himself to the idea that the Asuka in front of him wasn't real and that he was really and truly alone, only to be surprised that she wasn't a projection.