It would be great if there was a method (or two or three) to convert .eml files either when importing into DT to convert to .pdf or after importing them to .pdf. I can’t find a way to do it now but storing emails as .eml’s seems less useful to me than as .pdf’s.
Apple Mail’s File > Export to PDF… works well over here … albeit there’s a bug in 10.9.2 that drops the “.pdf” extension when more than one message is selected for export and we need to manually add the extension.
Email Archiver http://emailarchiverpdf.com is your friend.
Its a very good way to get your email into pdf as well as the attachments separated out into directories with the same name as the emails. This way Devonthink can search the attachments too