The thread seems old but for those who still haven't found any satisfactory solution should definitely try this Outlook PST to PDF wizard. This tool works perfectly and keeps the folder hierarchy intact. It also keeps the attachments embedded in their original format and provide multiple file naming options to save the converted PDF files.
If you are still looking for some solution to import PST files to Adobe PDF document without losing the folder structure then you must try PST to PDF Adobe Export Tool. This software will help you in exporting your PST files to PDF with all the email headers, formatting and folder structure in intact form.
For more information, you may visit : Convert PST Files to Adobe in batch