Solid point. I hadn't considered how it would be pronounced in German. Probably should have, but I missed it.The correct name is "Eva".
The reason she is called "Ēfa" ("エーファ") in Japanese is because they tried to follow German phonetics, where the "V" sounds closer to an "F". So "Efa" is more similar to how a German pronounces "Eva".
I think, for me at least, I imagine Eva to be spelled エブァ or エヴァ because of Evangelion. I rewatched the movies recently so it's been taking up space in my mind.
Most likely, if there is a correct way of spelling it, it's Eva. I'll probably be using Eva instead of Efa from now on.