It does break with standard shortcuts. And worse, there's absolutely no consistency between terminal applications on which shortcuts to use. It's a mess, and complaints are warrented.
Now, Super-C vs Ctrl-Shift-C (across the UI), we can argue about.
Ctrl-C (and Ctrl-Z, Ctrl-A, Ctrl-V and many other standard command-line shortcuts) have been around for longer than many of those users have been alive, and are part of POSIX standard.
The proof is in the pudding, though. I haven't seen any terminal apps that actually do what you praise (by default, as you can always remap the shortcuts to your heart content - to each their poison).
Micro editor, Emacs with CUA-mode.
Very few TUIs respect Ctrl-C. Note how it doesn’t quit your shell, for example. It’s more that it’s bound to something already, and there is no common concept of a clipboard between terminal applications anyway.
Asking the terminal itself to copy on Ctrl-C, and send Ctrl-C on Ctrl-Shift-C, is usually uncomplicated. If that’s something the user wants. We allow all sorts.