I am afraid there is no such "comprehensive list" of keyboard shortcuts. Keyboard shortcuts are conventions. Some of these are widely used, many not. The assignment of keyboard shortcuts can differ between operating system, between different desktop environments, and between applications. Gnome Shell prefers Ctrl+PgDn to navigate between tabs, in Firefox, it's Ctrl+Tab.
As a programmer, you certainly are aware of the following (you refer to it), but I mention it for completeness.
Keyboard shortcuts can be system wide, e.g. Alt+F4 to close a window. They will trigger the same action irrespective of the application in focus. They will eventually override the definition of the same keystroke at the level of the application (i.e., they have priority).
Other keyboard applications are defined by the application, e.g. Ctrl+q will be defined in many cases to quit the program. Ctrl+c will in the vast majority of applications be used to to copy information to the system clipboard.
None of these are set in stone, as you discovered. Ctrl+Shift+e in Ubuntu happens to trigger the entry of Emoj (at least it does not for me on Ubuntu 20.10), but that is not a convention that is widely used.
In short, no, there is no universal list of "reserved" keyboard shortcuts. As a programmer, you need to choose your combinations carefully. Don't worry too much. If you make the wrong choice at some point, your users will likely get back to you soon to fix it in an update.