If both the author's name and the pen name are known, should one cite by one name or both names? If one, which?
David Becker has written about APA citations for pseudonyms.
Citing pseudonyms can seem tricky at first, but it becomes much simpler when you take into account one of APA Style’s key mottos: Cite what you see. When it comes to citing an author, cite whatever name is used by the source, whether it be a real name or a pseudonym. For example, The Adventures of Tom Sawyer lists Mark Twain as its author, not Samuel Clemens, so you should cite the author’s pseudonym rather than his real name.
The full article deals with other peculiarities like titles (Dalai Lama) and how to distinguish Dr Seuss from Theodor Geissel.