The current version of phpdocx doesn't allow to encrypt DOCX files larger than 6.5MB. There's a warning about this limitation on:
When DOCX files are bigger than 6.5MB the workflow to encrypt them is diferent (XML files are splitted instead of encrypt single files). It's not a performance limitation.
PDF files don't have this size limitation when being encrypted.
It's a work in progress to support DOCX files bigger than 6.5MB that will be available in a future version of phpdocx, but there's no release date for it yet.