I'm using MacOS 8 and when I try to use the Ctrl key to access the ChemDraw Plugin menus, I get the MacOS contextual menu instead.
If you are using the Apple Data Detectors/Internet Address Detectors software version 1.01 (and probably earlier) from Apple, as you have discovered, you will not be able to use CTRL-click to access the Plugin menus. Apple released version 1.02 to resolve any CTRL-click conflicts experienced by customers. A word of caution that could cause some confusion. Version 1.0.1 of Apple Data Detectors includes Version 1.0.2 of the Contextual Menu Enabler (July 23, 1997).
The Control key is mandated by Netscape for all of their Plugins.