Warning: The following contains SPOILERS for Young Justice season 4, episode 9, "Odnu!"
Young Justice season 4 addressed the question of how it is handling the Captain Marvel/Shazam naming controversy, which was brought about by the complicated copyright feud between DC Comics and Marvel Comics. It did this by introducing the Young Justice version of Mary Marvel as an apprentice of Zatanna and referencing her complicated past as a superhero. This past was made even more complicated by Mary being unable to say what her superhero name had been for some unspecified reason, in what was clearly a clever nod to the show not wanting to mention their parent company's chief rival.
The controversy surrounding the original Captain Marvel (now called Shazam) and his name is one of the most fascinating and contentious in American comic book history. Captain Marvel was originally created for Fawcett Comics in 1940, but came to be owned by DC Comics following a lawsuit claiming Captain Marvel was a clear rip-off of Superman. DC Comics tried to start publishing new Captain Marvel stories, only to discover that Marvel Comics had copyrighted the name Captain Marvel for their own use. This led to an agreement between the two companies that DC Comics could continue to publish comics featuring the original Captain Marvel character and could use the Captain Marvel name, but they couldn't use the name Captain Marvel in any book titles or logos. This led to an entire generation thinking that the classic Captain Marvel's codename was "Shazam", which was the name of the wizard who gave Billy Batson the power to transform into Captain Marvel by saying his name. Rather than fight it, DC Comics retconned the character's history in 2012 and started calling Billy Batson's alter ego Shazam.
This controversy created some interesting questions for Young Justice, which featured Billy Batson using the Captain Marvel name in its first two seasons. The character was credited as Shazam in the one episode of Young Justice season 3 in which he had a speaking role, "Triptych," but his name was not said during the episode. The series finally addressed the issue in Young Justice season 4, episode 9, "Odnu!" which introduced the Earth-16 version of Mary Bromfield (aka Mary Marvel) as one of Zatanna's apprentices. The episode revealed that Mary was trying to find a way to express her magic powers as magic spells, rather than using her magic to enhance her body as she had in the past.
When one of Zatanna's other students, Khalid Nassour, asked Mary what Zatanna had meant when she'd said "you're still thinking too much like a superhero," Mary started to explain that she "used to be a superhero called Sergeant..." but then cut herself off before she could say the world Marvel. (Her original superhero codename had been Sergeant Marvel in the comics.) Mary then tried to explain that she had the power of Shazam, but had to cut herself off again before she said the name of the wizard Shazam and caused herself to lose her powers. Embarrassed, Mary admitted she couldn't actually say the name herself, allowing Zatanna's third apprentice, Thirteen, to mockingly whisper the name "Shazam" for her.
While this was all played for laughs and doubled as a reference to a running gag from the comics, where Captain Marvel Jr. couldn't say his own name as he had to say the name "Captain Marvel" to activate his powers, it was also a clever way of tip-toeing around the question of what name Billy Batson is using in the reality of Young Justice now. It seems that not only has Billy adopted the Shazam name on Earth-16, but that the show's producers aren't taking any chances using the name of DC Comics' business rival. Of course this hasn't stopped them from referencing their marvelous competitor in other ways, such as by parodying Spider-Man with the evil Black Spider.