There was an indirect mention of them when Batman confronts Harvey while he's interrogating Thomas Schiff. He says Dent is the first legitimate ray of hope in Gotham in decades, i.e. since the Waynes. But I agree that this is a perfect time for the story to return to them .
It's not an impossibility that the finger print would have been on the bullet. The casing doesn't cover the entire thing, a portion of the bullet is exposed and could easily have been touched by White when he was loading it into his gun magazine or whatever. Would it have made more sense to use the casing? Sure, but it may not have been around, and that story beat was there to further develop the sonar technology so that it would be used on a massive scale at the end of the film (which Batman did totally without Lucius by the way). Granted the technology itself is a little screwy, but c'mon, it's a comic book movie.