I need to start this off with the fact that Mary said in the beginning “if you’re watching this, I’m probably dead.” So she knows that, as she’s recording the video, Sherlock would be watching it after she died. Now anyone who can’t see the way sherlock looks at john, or how he simply acts towards him, must be blind. Mary surely figured it out from the start. And I bet she realised that if she died, she should let sherlock know that she knew, and that she was never against it, hence “i know you two. And if I’m gone, I know what you could become. Because I know who you really are.” She knew they loved each other, and although she really was in love with john, and he loved her, she still recognised the complexity of his relationship with sherlock. She still recognised that Sherlock was hiding his feelings, and John was struggling with his. She’s not dumb. She didn’t see, she observed.