I have installed KDE/Plasma 5.3.2 (non-overlay) on a Gentoo system inside a VirtualBox VM. I use Xorg with sddm as display manager and I have installed the latest VirtualBox guest additions. Everything is freshly installed, no modifications, only system defaults.

The issues that I have is that the bottom panel/bar and its menu disappears and so are all the windows in the desktop. The only thing that is visible is the desktop wallpaper and the icon in the top left corner. Sometimes also the mouse pointer disappears. When resizing the window of the VM, which forces the system to set a new screen resolution that fits the window, those above described elements temporarily come back and disappear again. Windows/panels that are opened by the icon in the top left corner don't seem to disappear the same way.

Does anyone know how to fix these issues, whether it should be reported somewhere and where? Or, should I go with the Overlay version of KDE/Plasma 5 and conduct the troubleshooting procedures there?

Try to disable 3D acceleration in the VM's settings.

There seem to be problems with this in VirtualBox (it is still labelled "experimental" in the documentation anyway...), and the symptoms are as you describe IIRC.

Yes, that fixed those issues, however I'm using 3d acceleration with KDE4, GNOME3, Unity, etc without any problems so it seems a little far fetched to blame VirtualBox for these issues.

KDE5 makes *much* more use of *much* more advanced OpenGL in *many* more GL contexts (QtQuick being the main driver here, but we also removed the OpenGL 1.3 backend from KWin) - it's very likely that this knocks out the virtualbox GL driver, yes.