I don’t know what a “folding header” is, but I do notice hits on Google with that as a search criteria. Perhaps get some guidance there as Markdown is not limited to DEVONthink. But, did you try? If so, what happened? Does it work with another Markdown editor that you prefer? Perhaps use that other editor, saving the *.md file into DEVONthink of course, if you need/want folding headers?
No, Devonthink3 does not have that functionality. While it could be useful for long code sequences to hide details of subroutines, objects etc., for long form writing I find that having the “Table of Contents” (open with CTRL-4) next to the markdown document does a better job. That is, it allows me to look at the grand structure of the document and jump around quickly.
Do have a play around with the Table of Contents function @Luminary99_0 has mentioned above. I had also wanted folding headers, but I’ve found that the sidebar contents list is more useful since it allows you to see all the headers whilst still navigating. Plus the function works the same across different file types, e.g. PDF, so I just find it easier as navigation is the same regardless of what I’m up to.
We discussed it in another thread a year ago and I thought you’d like to see the other conversation about it, as I was in your position and introduced to the functionality: