How do I remove log out, reboot, and shut down from GNOME shell application list?

If we talking about these gray colored icons:

then they are provided by session-shortcuts package.

We can hide them by copying to current user settings folder and then adding property NoDisplay=true here:

mkdir -p ~/.local/share/applications/
cp /usr/share/applications/{logout,reboot,shutdown}.desktop ~/.local/share/applications/
echo "NoDisplay=true" | tee -a ~/.local/share/applications/{logout,reboot,shutdown}.desktop > /dev/null

then logout (and login again) or reboot.