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Please note that hyphenation is supported by Aspose.Pdf.Generator namespace and Aspose.Pdf.Generator can only generated new PDF documents from scratch. In order to deal with existing PDF files (in your case PDF files generated with Aspose.Words), we have Aspose.Pdf.Facades and Aspose.Pdf namespace (this name space provides the capability to create new PDF as well as manipulate/edit existing PDF). But I am afraid adding hyphenation is currently not supported by Aspose.Pdf namespace. For the sake of implementation, I have logged this requirement as PDFNEWNET-34085 in our issue tracking system. We will further look into the details of this problem and will keep you updated on the status of correction .Please be patient and spare us little time. We are sorry for this inconvenience.
However as a workaround, you may consider using the Replace text feature, where you can add Hyphenation to words that are replacing current occurrences in PDF file. Please visit the following link for further details on Replace Text in All Pages of a PDF Document