LMDE 201403 Cinnamon 64bit
I saw posts over in Newbie Questions for Main Edition about the disappearance of the Update Manager icon from the panel ...
Well, it's happened to me on LMDE as well. Unlike the other case, I have not changed from the default theme. However I have used System Settings-Themes-Other Settings to select a different set of icons, gnome-colors-common. The item for Update Manager in the menu still has its icon (shield shaped).
Update : It's happened on LMDE installed on a netbook, but I've just checked and it has not (yet) happened on LMDE installed on a desktop. The 2 LMDE systems are very similar, that is, same level of Update and much the same additional packages installed, same additional icons installed and selected.
UPDATE I can live with this, I would assume that the icon will disappear from the panel on the desktop some time.