DEVONthink imports and stores files in their native formats. There is no conversion to any proprietary formats, nor do we have any. For instance, a PDF imported into DEVONthink remains a PDF.
Also, while files are stored in a proprietary folder structure internally, we provide many options for getting the files out. This includes simple drag-and-drop out of DEVONthink and the File > Export > Files and Folders command. It is also possible to access the internals of a database to access all these files in an emergency setting, but please contact our support team for assistance with this.