Interesting, it does seem that the use of dbus-update-activation-environment is not a full store reference in the NixOS module. I might recommend going ahead and filing this as an Issue on nixos/nixpkgs.
From what I can tell, this issue does not affect the home-manager module, as it properly references the dbus store path. I’m a bit surprised this hasn’t been noticed. I wonder if most Sway users are using Home-Manager? As you observe, this missing in the NixOS module means that non-HM-users are likely having problems with user services that expect certain env vars to be set in the user-systemd environment.
EDIT: Alternatively, it seems like you understand the issue. If you want to just fix this in nixpkgs, I’d be happy to review/merge it for you.