Nautilus seems to treat each hardlink as a separate file. Both on calculating 
size and on copying.
I just tried to copy a directory full of hardlinks and it makes separate files 
(KDE's dolphin file manager also does this). So, in a way it is consistent - if 
you were to copy a folder full of hardlinks with nautilus you would need that 
much space on the destination.

consequences:
huge size explosion if a folder with many hardlinks (e.g. the backup folder 
generated by the backup program "back in time") is copied
loss of some information: with find -samefile you can find the other names 
pointing to the same data (inode); that information is gone in the copy 
nautilus makes; 

All this is problematic. Nautilus tries to keep things simple. That's
why it does not offer a way to make hardlinks. But if things are already
complicated - if hardlinks are already present -  just ignoring them can
lead to problems of its own.

I do not know how to handle this comprehensively, but it might be a good idea 
for nautilus to at least display a warning.
That warning might also be used to tell the user that commands like cp -a can 
preserve hardlinks. 

** Summary changed:

- Nautiuls "File Operations" dialog does not handle hard links correctly when 
calculating size
+ Nautiuls "File Operations" dialog does not handle hard links well when 
calculating size or copying

** Changed in: nautilus (Ubuntu)
       Status: New => Confirmed

-- 
Nautiuls "File Operations" dialog does not handle hard links well when 
calculating size or copying
https://bugs.launchpad.net/bugs/644403
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