As with most things, the issue of who killed Beckett's mother is complicated. In "Sucker Punch" (Season 2, Episode 13), medical examiner Lanie Parish discovers that victim Jack Coonan has stab wounds similar to those of Beckett's mother. Forensic pathologist Dr. Murray determines that both murders are the work of the same professional hit man. Drug trafficker Dick Coonan, whom the team believes hired this contract killer to murder his brother Jack, is taken into custody and offered immunity in exchange for information. An elaborate setup is staged to capture a guy Coonan calls "Rathborne," but he never shows. Beckett figures out that Dick Coonan was the hit man all along and created Rathborne as a decoy. Coonan holds Castle hostage during his confrontation with Beckett, and she is forced to shoot him to save Castle's life.
SO, to sum it up: We know Dick Coonan killed Beckett's mother, but as Hyman Roth says in The Godfather II, no one knows who gave the order. It's only half-closure for the detective, since the person who did the physical work had no emotional investment in it. She still needs to find the man behind the curtain. In some weird way, getting the final answer to this would be like Beckett and Castle finally hooking up. They are two mysteries giving the show momentum. Once they're "solved," the show has to change direction.