I'm running on Wayland at this moment (Gnome 3 on Fedora), and just tested on the terminal. It has two: I can copy something with Ctrl-Shift-C, then select something else, then paste with Ctrl-Shift-V, then paste with middle-click; the selection didn't override what I had copied, and middle-click pasted what was selected.
So you still have two, at least with Gnome 3 on Wayland.