Tsukihime reference. Kohaku, a yandere, who plans to kill the protagonist and his family gets a happy ending where she smiled a real smile instead of the fake one used to hide her murderous intent, psychosis, and evil plots. So he asking to make sure she won't go back to plotting again.
It doesn't even need to be his concern about her going back to plotting. Shiki would be genuinely concerned for her happiness. She is ambiguous through the game, even after you have happy sex with her, she admits it could all be another ruse of her, or that she could even be deceiving herself. The 'happy' of her happy end is that she sheds the perception of herself as a doll she pulls the strings on she took to protect herself from horrible rape, and starts to live a life inside her own body where she can actually feel connected to other people. If she is still faking it, but just not plotting, or just acting happier, it'd be horribly sad.
