I think if an input field is hidden on a form, the value for that field won't be accessible elsewhere in the workflow unless the value is displayed in some other form field, such as a label.  However, form variables to do seem to be present outside of the form, regardless of whether they're displayed on the form. 

So, a workaround would be to create a form variable whose value is equal to the hidden field. Then you can reference the form variable in the Doc Gen action instead of the hidden field itself. 

There will be no values in the hidden fields. The reason is because those fields will be populated manually after the document is generated.

Got it - I misunderstood.  I don't think it's possible with the Generate Document action if you're converting the Word template to PDF. If you had it produce a Word document, they'd obviously be able to fill in the field, but I assume you're needing it in PDF form. 

Hopefully someone else can chime in and correct me!

Yes I may have to convince them to use a word document instead of a PDF.  I know the tagging is specifically for bringing over data from the form but is there a way to generate a word document from a word template and bring over  a hidden field from a Nintex form into a word document to be populated later manually if it wasn't previously created in the template?

When you say that the field would be "populated later manually", you're talking about someone going into the produced document and typing in the field, correct?

If that's the case, I'm not following where the Nintex hidden fields matter.  If you have a field in the original Word template that you don't want Document Generation to touch, I believe you just wouldn't tag the field. The produced Word document should leave those untagged fields untouched.