Rousseau never talked to Jin directly before the time-shifting and so never realized it was the same person. Jin was already on the raft the first time Danielle comes to camp to "warn" everyone about the Others. Jin was then with the Tailies for a long while. Jin and Danielle never came face to face, even briefly, after their time-traveling encounter. Therefore, there would be no Danielle not recognizing Jin, because she doesn't see him again.