I think it's up to interpretation - there are clear changes in her behavior that are noticed throughout the story, so maybe he does (and maybe that's what his dreams are trying to tell him) but refuses to acknowledge it or maybe he literally has no idea.
Even though you’re the Creator you can literally change it up having him figure out stuff making them at least advisor at least a bit smarter having his suspicion going up listening into the conversation or at least slowly starting to demand things from her maybe next time you put in she visits and stuff just small ideas I guess