Zero doesn't become a level E. He comes really close but chapter 46 or 47 he kills his twin and proves he is the stronger twin, so he gets all of his vampire hunting strength and that prevents him from ever becoming a level E. He also drinks the blood of his twin who had the blood of Shizuka, the pureblood who bit him, inside him solving both of his problems of weakness. But this is only so far there may be plot twists or something later on in the story since the series is still being written.
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Yes, Zero eventually becomes a level E vampire in Vampire Knight. This transformation occurs after he is bitten by a pureblood vampire and loses control of his bloodlust.