Hard links on High Sierra
The method you described involves installing a third party ln command that allows you to ask the kernel to create a hard-link for a directory.

The ln command from coreutils ends up executing the linkat() function in the Darwin kernel, where the source code includes the following comment:

/*
 * Normally, linking to directories is not supported.
 * However, some file systems may have limited support.
 */


It is therefore generally not recommended to create hard-links to directories.

In regards to upgrading to High Sierra, your system will usually have its file system converted from HFS+ (which supports these hard-links in some cases) to APFS (which do not supports directory hard links). Therefore you will not have hard-links after conversion.

See the documentation from Apple on the subject here:

https://developer.apple.com/library/content/documentation/FileManagement/Conceptual/APFS_Guide/FAQ/FAQ.html

Especially the following paragraph:


  Directory hard links are not supported by Apple File System. All directory hard links are converted to symbolic links or aliases when you convert from HFS+ to APFS volume formats on macOS.


The conversion program is supposed to convert these hard-links into symbolic links (soft links). The symbolic links points to new entries created in /.HFS+ Private Directory Data/.

However it seems that there might be a bug involving the conversion since you've experienced loss of files. This might be due to the fact that hard linked directories are seldomly used, and cannot be created with the standard Apple supplied tools.

Therefore I think you should file a bug report with Apple using Radar.