Re the Console icon - it will behave the way you describe if you have not quit the program. In the Mac OS, closing the last window of a program does not usually quit the program - it is still running. Try clicking the Cosole icon to make it the active program, then press Command-Q (Quit in the Console menu in the main menubar).
Re the icons disappearing, try scrolling the Launch Pad window sideways. If you are using a Magic Mouse, use a two-finger sideways swipe. Or, press the left and right arrow keys to scroll it back and forth. Or, click the dimmed indicator blob at the bottom of the array -