Unfortunately, subsequent pulls into either repository will break hardlinks for any files touched by the new changesets, even if both repositories end up pulling the same changes. Also, pulling with --rev never uses hardlinks.
You can recreate those hardlinks and reclaim that wasted space using the Relink Extension. Enable it:
[extensions] relink = # optionally specify the origin, if you do this a lot: [paths] default-relink = ../incoming
and run it:
$ hg relink relinking /home/hacker/src/incoming to /home/hacker/src/work collected 9999 candidate storage files pruned down to 5555 probably relinkable files relinked 4444 files (12345678 bytes reclaimed)
In Mercurial 1.3.1 and older (prior to Issue919), contrib/hg-relink in the source tarball can be used for the same purpose.