If you have the right to copyright under a pen name, should you not also have the right to sue without revealing your identity? A right that can't be exercised doesn't exist.
Rights can come in conflict with one another, and when this happens one has to yield. The public has the right to open court records, and defendants have the right to know who's suing them. These rights usually outweigh any right the plaintiff may have in suing anonymously. It is possible to sue anonymously in the U.S. (e.g. "Jane Roe" of Roe v. Wade was a pseudonym) but IANAL so I don't know by what standard this is determined or whether the TrueCrypt dev(s) would qualify.
