In addition to tar and pax...

Here's an example of converting hard links to symlinks:

http://cgd.sdf-eu.org/a/scripts/file/hdtosym
(It is too simple maybe since it doesn't search file system.)

Also rsync can handle hard links too.

Maybe build a list of inode# and complete path names of your filesystem.
Then any duplicate inode numbers remove (except the first) and create 
symlinks for the pathname pointing to the first.
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