The removal of X11 from Gnome was explained in the 2nd post of the update announcement (which, of course, should always be read before doing an update):
Hello community, here we have another set of package updates. Welcome to our new development cycle of Manjaro 25.1.0, code-named ‘Anh-Linh’.We will focus on Plasma 6.5 series and will introduce GNOME 49, maybe Cosmic 1.0 (Beta).
We managed to stabilize ‘Anh-Linh’ enough to release this update to our stable branch. However, users of Plasma and GNOME may lose their X11 session support. Therefore read our Known issues and solutions section before restarting your systems!
GNOME 49 is here and wayland is the default
With GNOME 49 there is no X11 session anymore. X11 support got disabled. It will get removed with GNOME 50 anyway. You still can use X11 applications via XWayland as usual, however running GNOME under X11 is not possible anymore.
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