Yes and no. X11 is the old window system for Linux (and most Unixes), but it was very much not designed with security in mind, and has become difficult to maintain to the point that the only new updates made to it are to help with Wayland backwards-compatibility. Wayland is its de facto successor, and most new Linux desktop development is based on Wayland rather than X11.
It really depends if you are using GNOME or KDE ( or something else ).
GNOME in Fedora defaults to Wayland already I believe. In Plasma 6, due to first ship in Fedora 40, support for Wayland will be complete. That is why they are targeting the switch for then.
Plasma 6 is KDE using the Qt6 GUI toolkit so the KDE in Fedora 40 will be quite different from the KDE in Fedora 38 today. Today, KDE is built with the Qt5 toolkit and only partially supports Wayland.
GNOME is built with a GUI toolkit called GTK. The current version is GTK4 and that will still be the version used in Fedora 40. GTK has supported Wayland since GTK3.