Interestingly, I received a .doc file this morning and double clicking it indeed opened it in PDFClerk, instead of in Pages as it used to (I do not have MS Word installed).
PDFClerk does let the system know that it can read MS Word documents, in exactly the same way that it lets the system know it can read PDFs, text files and graphics files. Yet those, on my system, and I have not heard otherwise from clients, still open in their respective most appropriate applications, i.e. not in PDFClerk. E.g, PDFs still open in Preview by default, and PDFClerk even claims to be an editor for those. So I’ll have to contact Apple and see if they have any ideas why for .doc files PDFClerk Pro is promoted to the default application.