This reads like two questions!

1. Word to html
A quick experiment shows me that save as filtered .html (with 'show hidden text' turned off) give me a file where hidden test is not visible; also, at least in my set-up, saving that html file as .pdf still does not include the hidden text.

2. Word to .pdf
Oddly enough, saving the same source from Word straight to .pdf does include the hidden text -- so I see more content in the .pdf than I do in the Word file with 'show hidden text' turned off.