Rick Borstein has posted an Adobe action file on his blog, Acrobat for Legal Professionals which you can use to export a list of the bookmarks used in multiple PDF files. Click on the link 'Download Create Bookmark Report Action' and download the file with the .sequ extension. Double-click on it and it will be imported into Acrobat.

The action will appear as an option in your Tools menu.

You browse and select multiple PDFs to process.

There's an option to select to generate .csv files with a list of the bookmarks.

The final result gives you a report like this which has .csv files attached for each PDF containing bookmarks.

Note that this action may cause the .csv files to be incorrectly generated with .pdf extensions if your bookmarks include underscores or other common delimiters.