ActiveHotkeys does not list common keyboard shortcuts such as Ctrl+C (Copy), Ctrl+V (paste), Alt+F4 (Exit app) and many other similar combinations. This is because they are not system-wide hotkeys. Instead, each application uses them internally (or does not, at its discretion).
ActiveHotkeys detects only global hotkeys, which certain applications register in Windows for their own use. Typically they are used to activate an application when it is minimized or hidden, or to perform other actions without having to bring the application to the front. When an application registers a hotkey, no other app can use that key combination for anything else.
Common keyboard combinations like those listed above are not global hotkeys. They could not be, because if Notepad registered Ctrl+C for “Copy”, you would not be able to use Ctrl+C in any other application as long as Notepad were running. Applications typically use these well-known key combinations for consistency, so that Ctrl+C and Alt+F4 mean the same thing in every program you use. But this is merely a convention, and nothing stops programmers from assigning entirely different shortcuts to the same functions. These keys are not globally registered in Windows though, so ActiveHotkeys does not detect them or list them.
(And yes, an application may reguiter Ctrl+C as a global hotkey for some function it performs. It would be a very bad idea to do so, of course. If an application does that, ActiveHotkeys will tell you.)