Ritsuko told him in 3.33 that it was as an insurance policy as well as a punishment. Keep in mind as well that when on the Wunder's bridge, Misato asks Ritz if it was really Shinji, she replies that it "seems that way." In a latter scene, they said that they are identifying him as Shinji "on a provisional basis." At the time, I found it curious that if their scans showed that it was really Shinji, why were they hedging their bets. It was these things along with some other scenes on the Wunder which led to the idea of the Ikari types.
Also, why did she insist on trying to have him fitted with it once he was in the city, when they should have confirmed by then that it was really him? It is very clear that she knows it is in fact Shinji, and still expresses concern for his well being - so why?
It was due to a combination of fear that he could still be a clone, an understanding of his nature both physical and mental, and some of her own issues in dealing with Shinji. I addressed these concerns both in Chapters 7 & 16, but perhaps I didn't do it clearly enough.