This is a thorny one, but absolutely essential.
The way we intend to solve these cases in BookBrainz is to have one single Author (with their pseudonyms as aliases for search purposes), and Author Credits applied to Editions in order to represent that a book was published under a pseudonym. This only solves the question of “who is this book from”, AKA who is on the cover, but does not solve all our problems.
It has been suggested to allow specifying a name in “Author wrote Work” relationships, meaning entering a relationship as "Author X wrote Work Y credited as ‘MyPenName’ " like this (using MusicBrainz as an example):
This is the ticket where we’re tracking all this: [BB-475] Work relationship credits - MetaBrainz JIRA