It's quite possible that they're loaded in /etc/rcS.d. However, manually editing that is not the best method for achieving your goal for a few reasons:
1. Your startup files are no longer standard which can cause all sorts of wierd problems.
2. When a new version of freeswan (or openswan, actually) comes out, if you're not paying attention then all of your changes can be overwritten by the new package.
I myself don't have [free,open]swan installed but usually there is a config file somewhere in /etc (but not in /etc/init.d or /etc/rc*) that will control all of a package's behaviour.
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