It didn't seem like she was crying because she remembered but because DiZ gave her hope that the boy that Mickey mentioned and she met all those years before is alive and well and protecting the worlds from darkness. There is also hope that he will be looking for a way to get them out of there and restore order, hence the tears IMO.
About Terra and Ven. We don't know how much time passed from the ending of 0.2 until Blank Points. It's at least a year in real time. She doesn't know what is happening it makes sense that her first thought when she hears "a boy with a key" would be Ven or Terra since they both fit that description.
Not when she personally knows that last she saw them they were both incapacitated and Mickey told her that Sora was active. The fact that he isn't the first thing she thinks of does not make sense now. The fact that she asks about the worlds being in danger doesn't make sense now.
It's like people jumping through hoops trying to explain why possessed Ven had blue eyes till the patch in the opening, or Donald and Goofy acting like they don't know who the fuck Yen Sid is in 2. Or Namine somehow being the one to tell Terra about Aqua when there is no timeline where that makes sense.
No there isn't a justification, KH just fucks up its continuity all the fucking time.