Though I believe Aquaman disappeared from the last group of JLU episodes due to that Aquaman pilot. Which is why Black Manta was renamed.
I thought it was because there were concerns about the racial implications of the name. Though such concerns have evidently faded by now, since Black Manta has appeared twice in
Batman: The Brave and the Bold.
Its just silly honestly, like the movie going public and the cartoon watchers are going to be "confused". Heck, I don't remember any such embargo against any Spider-Man cartoons or X-Men cartoons when their movies came out. And each cartoon had a different continuity too.
Well, as I said, WB only seems to have a problem with two animated or two live-action versions existing at the same time.
And maybe the concern isn't with actual watchers of the shows/films being confused, but with the respective promotional campaigns being confused. If you're seeing 30-second promos and print ads and such for two different live-action versions of the same character, it could be harder to tell which is for which. Not sure if that would really be a problem, though, since it would presumably bring more attention to both. But maybe if people blur the two in their minds and assume they're for only one thing, then they might go to the movie and skip the show, or vice-versa.
Sometimes, though, studios don't like overlapping versions of the same story regardless of medium. The '90s
Spider-Man animated series was initially forbidden to depict Spidey's origin or feature Electro and Sandman, because those were elements of the James Cameron feature film that was in development at the time. Once the film fell through, the show got around to doing Spidey's origin, and in its final season it introduced a version of Electro, though Sandman never appeared.