Will this enhancement convert all the existing links or only the links posted after the upgrade?
All existing links.
Is there a way to set these hyperlinks to open in a new window?
They already do if it is an external link.
Is there any way to create a security option, so people know what link they are going to?
This has nothing to do with auto links. If it is already a link we don't touch it. Which means you have already taken the risk of letting unknown users enter html.
We may add an option to redirect all external links to a dispatch page that warns the user they are about to leave the site. Beyond that, not much else we can control.