An easy way of creating nicely-formatted html files from DT items written in Markdown is to use Strapdown.
Simply create the following export template as an html file in DT’s websites folder (e.g. in ~/Library/Application Support/DEVONthink Pro 2/Websites):
<!DOCTYPE html> <html> <title>%title%</title><meta charset=%charset%> <xmp theme="cerulean" style="display:none;"> %content% </xmp><script src="http://strapdownjs.com/v/0.2/strapdown.js"></script></html>
Then select your Markdown items in DT, choose the menu item File/Export/as Website… and select the export template you created. You can choose from 11 different themes for the resulting html files that are saved. Simply replace the theme name (cerulean in the above example) by one of the other names shown on the Strapdown website.
As a bonus, use the DT menu item Data/Create Table of Contents to create an index file and add that into the selection that you export (or else you can create an index as part of the Export as Website dialogue).