- Manage it out of band. That negates all of the benefits of NixOS, at least for those files. (I.e. you would need additional deployment steps, rollback wouldn't work, you would have to stop and migrate system services that depend on those secrets yourself, etc.)
- Encrypt it and only decrypt it on activation (which happens when switching to a new config or on boot). agenix and nix-sops (the premier SOPS/NixOS integration) are two libraries that you can include in your config to do that. With this, the world-readable store only contains encrypted secrets.
Of course with #2 you still have to manage your private keys (age or whatever SOPS uses) out-of-band but that is significantly less work since those aren't expected to change nearly as much. You can also generally decouple that from your day-to-day deployment workflow.
In terms of NixOS integration, both are on equal footing.
I'm just unfond of yaml is all.