OK, so... This is somewhat related to binary cache self-hosting... For context - I've been experimenting with setting up a solution for automatic/transparent local cache sharing across machines in the same LAN, via avahi-based wrapper around Harmonia. This worked great during my initial testing.

Now I've noticed that somehow most of the paths in my local nix stores (ones that I am 99% certain were pulled from https://cache.nixos.org) don't actually contain any signatures (looking at Harmonia narinfo / ValidPaths table inspection in /nix/var/nix/db/db.sqlite). If I manually run nix store copy-sigs --all -s https://cache.nixos.org/ I see cache.nixos.org-1 signature for all the paths I check again. Any new paths that were just fetched during eg. nix-shell -p ... also have correct sigs...
I see this behaviour on at least 2 vastly different configs, on different long-running machines (nix 2.18 & nixos 23.11, nix 2.28.4 & nixos 25.05) - db.sqlite usually has sigs for ~10% of paths (1747/13143, 2790/22476 - after nix-collect-garbage + copy-sigs on latter mentioned above it's up to 9938/19420)

Any idea what could be a reason for that? Maybe some GC/optimise-related behaviour? I had a quick glance at cppnix source but don't see anything obvious...
I'll go back to trying to reproduce this, but if anyone has any hints...