Michael, did you ever find out how to solve this problem? I've got the same problem.
-- Tom Dayton
Michael, I've got one solution that meets my needs but maybe only part of your needs:
Buy AutoBookmark from Evermap: http://www.evermap.com/autobookmark.asp#Creating%20Destinations%20From%20Bookmarks
It's a plugin to Adobe Acrobat (not Reader), but it works only in MS Windows, not Mac.
After you've installed that plugin, Acrobat's Plug Ins menu has a Destinations menu item with some choices you're going to use.
Open with Acrobat, the PDF file that has the destination names that have that bothersome <filename>.indd prefix. Use the Plug Ins > Destinations menu's item to export the destinations as a plain text file.
Edit the resulting plain text file with any plain text editor. Globally search and replace the filename prefix with nothing. Save and close that file.
Back in the Acrobat window of your PDF file, use the Destinations menu's choice to delete all destinations.
Now use the Destinations menu to import the destinations file you just edited.
BUT the part of your problem that this won't solve, is the presence of a portion of the sentence in the destination. That's not a problem for me, because I'm creating all my destinations as parts of the sentence.