I've added an encrypted PDF file to iTunes and synced it with my iPad.
Before doing so, I opened the PDF with Adobe Acrobat Pro and edited the metadata to include the document title (which is identical to the filename). I then password-protected it, selecting the option that encrypts all content except for metadata.
In iBooks, the PDF is displayed with its correct title in Library view but when I input the password and open it, the overlay text in Reading view says it is "Untitled".
However, if I add it to iTunes as an unencrypted PDF it displays correctly in both Library and Reading view.
I would prefer it if I could keep this file encrypted. I know it's just a minor inconvenience but I can't see why the title should fail to display in Reading view once I've opened it.