1) Yes, please update to the öatest release.
2) ISPconfig 3 updates a site only when you change something in the ispconfig interface and not when the server is rebooted. You can verify that by enableing debugging in /usr/local/ispconfig/server/lib/config.inc.php and then check the monitoring module after a reboot. If ISPConfig updates your sites then there will be a lot of lines which describe the update process for every website in detail.
3) The vhosts files should never be modified manually. Either you edit the master template that is used to create the files or you add your modifications to the apache directives field of the website.