My take on the Third Eye power is: unless you're relatively powerful in the Third Eye department and/or you use a spell card, you can only pick up what the other person is thinking this very instant. You can't detect ignorance or completely search their mind, so Koishi wasn't aware that Flandre didn't know about sex (and assumed she just didn't realize it at first) until, um, she discovered that Flandre was thinking complete and utter "hang on wait what is this I don't even" about ... stuff.