My hat off to you. I read your critical analysis of my joke and for a few minutes thought you were serious.
I think it's a fair reaction to be mildly annoyed when someone uses something within your field without any real understanding what it does.
After all, programmers are one of the first to point fingers and laugh when e.g. movies use random code snippets or wrong jargon. One of those "Periodic Table of X" things is basically the chemist equivalent of Saying "I'll write a GUI in Visual Basic to track the killer".
This website has a different purpose though, as many people note.
If someone made a map of the US with only cities that have repositories named after them highlighted or some such thing would reasonable geographers think, "this is meaningless! They don't even understand what a map is!" (I hope not).
It's something for fun, and not presenting itself any other way... It's not even "abusing" the period table format for some other data (when I saw the link I thought it might be related to languages used on GitHub), it's literally mirroring the names of the elements that are in the real table but linking to projects with the same name...
Sometimes I just don't get some perspectives on HN--if I were a chemist who also knew that naming things in software is hard, it probably would have made me chuckle not furrow my brow.
Edit: missing word
I think it's cool, by the way.
I think it'd be even funnier if the repos it links to weren't even named after elements, but just had names resembling the abbreviations or something. But then again, it would be hard to find some more useless grouping criterion than being named after an element... I wonder if it's actually worse than random :)