>>2338651Gendo didn't visit Rei, only Shinji did. There's a lot going through her head, and so few actually stop to consider that Rei is a person who has just been brought back to life. She knows she has died, and she has been replaced, which definitely cuts deep into her psyche.
That's why her lines go "Because I'm the third.".
It's amazing that Rei wasn't bawling before she started crushing the glasses. The feeling Rei has when she's crying earlier, is that she's hurt and lonely and those emotions are finally coming out.
Rei is still as hurt and lonely as ever when she's Rei III. Only she doesn't consciously remember the revelation, but her heart does.
She doesn't cry for missing memories, but she is missing some and can't actually remember having shed tears before. Her full lines go:
"These are tears?"
"This should be the first time I've seen them, but I feel like this isn't the first time."
"Am I crying?"
"Why am I crying?"
