Hi!
I was stung by the bug that Gnome boxes Flatpak version cannot share USB devices because of sand-boxing. So I deleted and proceeded to install the Yast version and discovered that it disappeared from the Application launcher in Gnome.
This might be partially helpful. It’s necessary for the USB and other peripherals to work with OpenSUSE for the repo version of Gnome-Boxes. Might be similar for the flatpak version too.
If you’ve not already done so, be sure to open up the User and Group Admin section of YaST.
Click on edit and then details. Click on kvm, libvirt, and qemu boxes.
Then reboot.
What exactly do you call “Application Launcher”? Is it App Grid that appears when you click Activities - Show Applications? In this case Boxes is most certainly there, it is just that App Grid is not sorted alphabetically, so icon may be in some unexpected place.
If you mean something else, please describe in more details.