WebCam Monitor has no effect on Windows Live Messenger.
It is possible that when WebCam Monitor displayed its icon in the System Tray (at the bottom right of your screen, a part of the Task Bar), the number of icons there became too large and the Live Messenger Icon is no longer visible. To check, click the "Show hidden icons" button (the left-arrow in a circle at the left edge of the System Tray), which will expand the Tray and show all icons.
You can change which Tray icons are normaly hidden using the Task Bar settings.