If you have to include “the list”, your example, although acceptable, feels a little inelegant to me. I would prefer to associate “name” and “list” more closely:
Why is her name on the list crossed out?
This reduces the sentence to two ideas, making it snappier.
Another possibility is to change the preposition to “from”, which conveys the idea of removal:
Why is her name crossed out from the list?
However one might argue that this is illogical as the name is still there, even though it has a line through it.
In this case one might cast the whole sentence in a figurative sense and say:
Why has she been removed from the list?
The act of crossing out her name on a paper document is equivalent to removing her from the collection of people listed there.
But it’s really a matter of individual stylistic preference.