DEVONthink uses pdf2text to extract the text portion of PDF files, and so password-protected PDFs make some trouble here as they won’t allow pdf2text to access their text. When you import such files into your DEVONthink database, they appear normal at first, but are not searchable. Also, you get a log entry that tells you that the PDF file contains “no text”.
A cheap solution for this problem is Michele Balistreri’s “PDFKey”. This small app allows you to print all PDFs, even if they are protected. So, you can use PDFKey to “print” a PDF file into a new PDF that is both printable and editable – and the latter allows DEVONthink to extract the text for searching, classifying, etc.
Here’s the link: pdfkey.tk