Some of the tie in comics did expand upon her backstory. Your comment prompted me to go back and re read them so I might as well drop my mini reviews of them here:
Batman & Robin Adventures Annual #1: The story involves a villain named the Hypnotis, a villain from the days Bruce trained with Zatara who returned to steal a mystic gem that Zatara trusted Batman with years ago. As you might have guessed, the villains power is mass hypnotism and he believes the gem will enhance his power. It's primarily a Batman and Robin story but we see that Zatara has actual magic power in the story and Zatanna appears in the latter half of the story and helps defeat the villain. We see her do magic but it's not the classic backwards magic but a made up incantation. The story was good but the art was kind of muddy. Joe Staton is a great artist but he does not have it in him to ape the DCAU style. The story was written Hilary J Bader who wrote several episodes for several DCAU shows.
(Side note: the story is connected to Superman Adventures Annual #1. Zatanna doesn't appear in the latter save for a one panel cameo but it might interest Superman fans since it features Superman meeting Zatara and trying to learn magic in order to better defend himself against it and he even uses the same code name Bruce used when training with Zatara 'John Smith'. It also features his first meeting with Dr Fate. There are points where both Annuals interwine but both stories can be read on their own. Personally, I thought the Superman story was all over the place while the Batman one was better and more straight forward.)
Justice League Unlimited #40: This is her best appearance in the DCAU. Written by Ben McCool with art by Daniel Brizuela.
It's really good because:
-She's the lead character of the story.
-The story gives us a semi explanation for why she didn't have her powers in her first DCAU appearance: when Zee was young she misused her powers so her father took it away 'until the right time'. As she grew older, her powers started coming back.
-The real villain of the story is a Zatanna rogue: the Warlock of Ys. no
-References to Zatanna's Search, the Homo Magi and even the Medulla Jewel. I would read a whole spin off done in this style.
-No unnecessary romance or her pining for other characters.
-She saves the day. In other words, it's the complete opposite of her YJ version. I really wish this had been the basis for her character arc on the show.
-Also I thought this moment was cool:
Other notable stories:
Justice League Unlimited #14: This is more of an ensemble piece and features Zatanna, Deadman, Phantom Stranger, Dr Occult, Zauriel and Etrigan traveling to limbo to free the dimension from the Demons Three.
I would love to read a JLD book with this roster. Everybody got to shine here.
-Etrigan and Zauriel as bickering rivals was an interesting and I would love to see more of it. One of my problems with the current JLD book is the lack of group chemistry (even John/Zee feels forced). Even though it was one issue, the group dynamic really worked; Etrigan represents darkness, moral ambiguity, a trickster whom you can never be sure is fully on your side with Zauriel as the dutiful soldier whose dedicated to his cause, Deadman is the trickster, Zatanna is the moral center, Phantom Stranger is the wise sage and Dr Occult is the older veteran.
-The Demons Three wanted to tap into Zatanna's power and channel it as a means to destroy the rest of the team which is a huge cred to the kind of potential her power has. Zatanna is also the one who tries to hold the team together when Etrigan and Zauriel start going at it.
-Everybody contributes to the resolution.
Justice League Unlimited #1: This is more of an ensemble story involving the League's physically most powerful members experiencing bouts of possession during which they end up causing destruction, with the exception of Zatanna who was present. I initially thought the resolution was going to be that Zee wasn't possessed because magic is a learned skilled and possessing her would be the same as possessing an ordinary human woman but turns out the villains were just jerks and didn't think that anyone besides Superman, Captain Atom and Wonder Woman were worth their time (boy were they wrong).
Justice League Unlimited #41: This is the 'Joker invades the Watchtower and Zatanna, Hawkgirl, Crimson Avenger and Elongated Man have to stop their rampage' issue. It's a fun one off issue. Also subverts the 'gagged and helpless' trope that often plagues Zatanna since she manages to punches him out after she gags him. Also found it amusing that the Joker was like 'shit she can run that fast in heels?'.