I use CS3 versions of Illustrator and Indesign on an external Drive A running Yosemite without any problems.
To test whether my CS3 applications would work under El Capitan, I cloned Drive A to another external drive, Drive B, using SuperDuper and upgraded Drive B to El Capitan. I had to install Java SE Runtime(?) before the CS3 applications would open under El Capitan. Illustrator CS3 opened and printed without any problems.
InDesign CS3 opened with a dialog box saying “The Workgroup Client.IndesignPlugin plug-in conflicts with Workgroup Client UI.InDesignPlugin. Try removing one of the two plug-ins from the PlugIns folder and restart Adobe Indesign.”
Clicking the “OK” or “Don’t show me this again” buttons brought up a second dialog box that said “The Workgroup Client.InDesignPlugin plug-in conflicts with Book.InDesignPlugin. Try removing one of the two plug-ins from the PlugIns folder and restart Adobe InDesign.”
Clicking “OK” opened a third dialog box that said “The Workgroup Client.InDesignPlugin plug-in conflicts with Workgroup Client.InDesignPlugin. Try removing on of the two plug-ins from the Plugins folder and restart Adobe InDesign.”
I had to force quit InDesign because that was the only way to quit the application.
Since Workgroup Client.IndesignPlugin was the problem plug-in in all 3 dialogs, I removed that plug-in. (The plug-in can be found by using the Option key while right-clicking on the Adobe InDesign CS3 icon, choosing Show Package Contents, and following this path Contents:MacOS:Required. Workgroup Client.InDesignPlugin was in the Required folder.
I moved Workgroup Client.InDesignPlugin to another folder on the external Drive B and relaunched InDesign. It opened and I printed a page from one of my documents. I don’t know the function of the plug-in so PROCEED WITH CAUTION. I don’t use the application regularly so I haven’t tested the application extensively or run into a problem. A problem is probably out there waiting to strike.
TRY THIS ONLY IF YOU ARE ADVENTUROUS. Perhaps someone knows the function of that plug-in and what might happen by removing it.
Hope this helps and above all, this is only my experience, yours may vary.