Note
folders on one file system which have been hard linked together
Usually in Unix hardlinking directories together is not supported. I assume you mean "files in one directory are hardlinks to files in another directory".
mv behavior
Let's say you have many files hardlinked to each other, i.e. many paths leading to the same data stored once within the filesystem.
Compare this Unix & Linux SE answer. The relevant part:
A move between filesystems (it doesn't matter if it's on the same physical medium or not) is handled as a file copy followed by a delete. This is in fact exactly what the mv command does. Obviously that means that the destination filesystem has to make a new copy of the file.
After a copy is made, mv removes the source similarly to rm. This applies:
rm simply deletes the pointer. If you have multiple pointers to the file (hard links), then deleting one of those pointers with rm leaves the others completely untouched and the data still available.
So if you move few of the hardlinked files to another filesystem, other hardlinks will be safe. Hardlinks cannot cross filesystems so the new copy cannot be a hardlink to anything that is left on the source filesystem.
If you move all of the hardlinked files, they will all disappear from the source filesystem and appear in the target one. Be aware that even a single mv (moving multiple files) will create every new file separately, they will no longer be hardlinked to each other. In theory mv could perform some additional work to detect hardlinks and recreate them in the target filesystem, it just doesn't (as shown in this another answer).
Moving hardlinks to get hardlinks
There are other tools that do recreate hardlinks, tar is one of them (although I'm not able to tell if tar on Mac OS X is for sure). Compare this:
By default, if you tell tar to archive a file with hard links, and more than one such link is included among the files to be archived, it archives the file only once, and records the second (and any additional names) as hard links. This means that when you extract that archive, the hard links will be restored.
Note that hardlinks will be restored between the restored files (i.e. they will mimic the hardlink connections of the source), but the restored files will never get re-hardlinked to source files (or their hardlinks that may still exist), even if they are extracted to the same filesystem tar got them from.
To make advantage of tar without creating a large archive you need few shell tricks. E.g. :
tar -c /source/dirA/ /source/file1 | { cd /foo/destination/ && tar -x; }
The command performs copying without deleting. If you need to delete the source, do it with a separate command eventually.