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It seems like most of them do[1] (inc. ext4, zfs, btrfs), but they’re fairly limited in size (but should be fine for media tags and such).

[1] https://en.wikipedia.org/wiki/Extended_file_attributes#Linux

They do.. but integration is almost nonexistent.

All e-mail were separate eml files, with attributes for most of the important data.

Same for contacts.

In BeOS everything was more a file than in most *nix

Of course a built-in would be nice, but I think one could get 99% of the way there just with a specialized scanner (that I don't know the name of) that kept its own database, like CTAGs or the old OSX Quicksilver (and probably Spotlight after it).

Not unix-y but OS/2 had something similar.