Use a template-based configuration management system to pull in secrets from a secrets management system (passwords/credentials/PKI management). It's an antipattern to add even more complexity by bolting on configuration or secrets management as part of nix, systemd, or anything else that's OS- or distro-specific. Package managers, and OSes need to offer sane defaults but then have sensible boundaries and allow configuration responsibility to be delegated to users and/or configuration management.

Who other than nixOS has this problem? Feels like a nixOS thing to me, which I'm not going to complicate my applications for. All the orchestration tools have something like a vault, don't they?

Happy to be shown wrong though.