Sorry... I said nonsense.

Hardlinks ARE working. I have installed Link Shell Extension 
(http://schinagl.priv.at/nt/hardlinkshellext/hardlinkshellext.html) and it 
displays .hg contents as HardLinks (red dot overlayed over the file icon).

Then, maybe the problem is that the CGI script treats directly some .hg file 
as a hardlink without making a local copy when things on only one repository 
change (making both repositories appear to change)? It works with internal web 
server, so the problem should be at the CGI code.