Hardie Board Subfloor—Thinset or No?
The installation manual for HardieBacker suggests to embed it in thin-set and it should be installed over plywood. 

Thus I would suggest removing the current wood planks flooring, install a 3/4" outdoor grade plywood, thinset and then your HardieBacker (screwed down). 

All of this is to prevent as much movement in your substrate and avoid cracks in your tiles and in your grout. 

Here is the link to the installation guide: http://www.jameshardie.com/d2w/installation/hardiebacker-us-en.pdf