In the past, I think people have recommended integrating with netdata. I don't have experience with netdata but wanted to throw the idea out there. Other than that, current graphs is rendered using data collected by graphite/carbon.

Hi, I do not have any experience with zabbix, but the agent looks like it would not interfere with system configs or updates, so it should be ok to use that. Cloudron itself will update packages where it makes sense through a Cloudron version update. However security updates are applied automatically in the background (this is also the reason why your Cloudron will sometimes show a notification about a required reboot)