Hardlinking in Linux is an option only if the files reside on the same file system.
There are tools for deduplicating directory contents by hardlinking, such as the excellent
https://jak-linux.org/projects/hardlink/ and it is included at least in Debian. Chances are your ${DISTRO} has binaries too. I am using hardlink in a different scenario and for me it works as expected.
But i'm not really sure if externally messing with hardlinks might result in Calibre to unexpectedly wreak havoc with your precious files...