I pick this discussion up though it is already old. I have the same problem:
In DEVONthink my Markdown files are listed as the document type “E-book”.
The solution described in this discussion does not work for me. All my markdown files are categorised within Finder as the file type “markdown”. Moreover, all these files are set to be open with “DEVONthink 3” as the standard.
So, any other ideas what I can do to change the file type from ebook to markdown?