OpenVAS is a vulnerability scanner that appears to be open source.
Metasploit is another that I think is free and might be open source.
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Instead of trying to automatically scan your environment, it's probably better to figure out how to automatically update applications first. CVE's eventually get patched.
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I'm not sure about cert scans, but ShadowServer is what I use for automated scans. They're free and the scans are thorough: https://www.shadowserver.org/what-we-do/network-reporting/
There are variouse alternatives to see what ports are open. Usually they autyo scan just the ip you come from, to avoid being used to scan a potential target.
If you want more, just use Greenbone. Run it twice. Once from another IP just to know how the world sees you. One time internal network and add accounts to greenbone allowing it to login and check further.
If you run linux, then Lynis is awesome to verify your config
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Second comment, but also investigate Wazuh. It can audit systems and report vulnerabilities. It's not an external scanner, but I have found it to be more effective and less annoying than greenbone/openvas.
Are you just wanting to scan certs? LetsEncrypted partnered with RedSift to offload their cert expiration checks. It's free: https://iam.redsift.cloud/signup?product=cert-letsencrypt. Uptime Kuma will also track your certs too.
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