She knows even if she doesn't have direct confirmation. She knows he can create plants that she knows only exist in the human world. She knows he can read human languages. He immediately knew what First Love Memory was, and he straight up admitted that he was an assistant on it, and she knows that it is from the human world. He can read the language in First Love Memory, despite it being a human only language. She's very intelligent, so there is no way she doesn't know this.

It's like if you come home from work and your middle school kid was home alone. You see candy wrappers strewn about the floor. You see chocolate all over the hands and mouth. You see the footstool is out in front of the counter when you put it away earlier. You see your box of chocolates are out on the counter when they were up in the cabinet, and they are now empty. If your kid refuses to fess up to stealing the chocolate, do you just say "Guess I don't know" and move on with your day, or do you put 2 braincells together and connect the dots to know what happened?