I think Alexandra Elbakyan actually did not want to be revealed as the librarian behind Sci-Hub, it was her poor opsec that led to her being identified.
Basically her servers were set up to emit detailed error messages from PHP, including full path of faulting source file, which was under directory /home/ringo-ring, which could be traced to a username she had online on an unrelated site, attached to her real name. Before this revelation, she was anonymous.