> Interestingly, at least in my browser and grabbing the direct link to the comment with curl, show the bytes as 0x20 for both. Perhaps the comment submission handler, or even the browser, collated your more specific U+2009 (thin) and U+200A (hair) spaces into the regular U+0020 space?

Probably! I think HN strips out emoji; maybe it just takes the safest approach and strips out all non-white-listed Unicode.