First thing you should do is copy the original configuration file to a save location so you can customize it. ISPConfig has a built-in conf-custom folder. When ever a file is places in there, having the same name as a server/system/ISPConfig config file, it gets overwritten:
cp /usr/local/ispconfig/server/conf/nginx_vhost.conf.master /usr/local/ispconfig/server/conf-custom/
Now you can edit the copied file:
You'll find parts like this:
Everything in there will only be applied to SSL enabled sites. So you could create 2 "master blocks" like:
(everything SSL goes here)
(everything non SSL goes here)
That way, you can have two different ways ISPConfig creates the vhosts.