It's an interesting anomaly, but I think it is mainly due to the fact that the look of almost everything changed after CE.
Of course, you could ask the same question for the assault rifle and other small differentials of similar changes, But they have officialy ret-conned the assault rifle to have more than one model.
While I think it would be less likely to have a second model of the Wraith, it certainly is a possibility.
I would advise that you watch for the Reach/2/3 Wraith in CE Aniversary, As I have already seen certain changes that make the game look much more similar to Reach's graphics.
Also, a major reason for their appearance differences is the fact that Bungie could do so much more with the graphics of Reach than the previous games. Plus, the reason the assault rifle is different between Halo CE, 3, and Reach is because they are different models along with the above. The Halo CE assault rifle is the MA5B, the Halo 3 version is the MA5C, and the Halo Reach variant is the MA37.