If for some reason, those options do not work exactly like you need them, then mkisofs or whatever tool you use must be improved, not the file system. I have a lot of experience but I have never seen any application for which hard links are the best solution, but I have seen a lot of cases when they are an inconvenience.
I must make a correction to the article, the phrase "the idea of "hard links", known simply as links before symbolic links were invented" is not true. The first type of links that were invented were what are called now symbolic links, and they were introduced in the Multics file system.
UNIX made four simplifications of the Multics FS and the last two of them were stupid (i.e. they made negligible economies in time & space, but they created problems that are not solved even today in the successors of UNIX):
1 Short 14-character names instead of long names
2 A single set of file mode bits instead of ACLs
3 Hard links instead of symbolic links
4 Merged write & append rights
Later, BSD did the right thing by reintroducing in their improved file system the long names & the symbolic links, which were copied afterwards by the other UNIX derivatives.
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