Clone Wars isn’t a part of EU though it contradicts EU and the lore and canon established. The Genddy series fits in EU. Filoni does not. They could do all the edits they wanted to try to bring Filoni into EU before it was moved to legends and they never worked. I always despised the Mortis arc in EU. It made Crucible a novel not worth reading.

As to whether they never brought Hayden in to dub Anakin in the cartoons I have no idea why? I do enjoy Matt Lanter so much more than Hayden it’s another level. But Hayden was so good in the new shows. Why didn’t that show in the prequel. Except in some places, it’s like George had him read his lines with as little emotion as possible flat and bored.