Rumors

Long answer: While Kanzaka has made a point of NOT confirming this rumor to be true, he also seems to make a point of throwing out more clues. Let's recap.

• When Lina laughs like Naga, Amelia tells her it reminds her of her sister.
• In episode #17 of the first series, right after Gourry and the others show off their new disguises, someone dressed like Naga walks by the camera, and Amelia double-takes.
• Aside from that, you never see Amelia and Naga in the same place. They both show up in both Slayers Royal video games, but never in the same scene. Naga meets Gourry, and occasionally even Zelgadis, but never Amelia.
• In Slayers TRY, when Amelia and Gourry are walking arm-in-arm, Gourry makes the comment that Amelia's getting taller. She notes that her older sister is about Gourry's height. (Let the record state that Gourry is about the same height as Naga.) [Special thanks to LinaxelzelAlly]
• There's probably a lot more instances, I can't remember them offhand. (Email me if you know?)

In any case, there's proof. Lots of proof. And when you don't deny something is true, it most likely is. ;)

Long answer: According to QP/Diana, there is no additional official information about the death of Amelia's mother. However, on the Japanese webpage titled "The Mega-Brand Project" (named after the spell, of course) there is an interview with Kanzaka in which he "revealed that Phil's wife, the mother of Gracia (Naga) and Ameria, had been killed by the assassin Booley. Gracia saw her mother die and killed the assassin with her mother's original spell, Chaos String. The author hasn't revealed the background of this bloody tragedy, who had ordered Booley to kill the members of Saillune family. Mr. Kanzaka said in one interview that the cause of tragedy was in the problem in the royal family. This is the only explanation about the background of the death of Gracia's and Ameria's mother."

QP/Diana also has additional information about the related rumors: " The rumor of Naga's being the intended target is the imagination of some fans. They say that when the person who hired Booley had wanted the throne, the target would have been someone being in the line for the succession to the throne. Phil's wife wasn't the one, so she couldn't be the target. Some fans believe that Gracia was the intended target, since only Gracia saw her mother being killed. Mr. Kanzaka confirmed in one interview that Gracia was in the room of the tragedy when her mother was killed, but Ameria wasn't. I think this theory is logical, but still it is a rumor, not the official information, nor the confirmed secret in the fanclub."