Close window shortcut & missing icon in top panel

@NicoBeno, welcome.

Can you check in 'Keyboard Shortcuts', if there is another action using same shortcut key combination (Alt+F4).

The two network indicators are from 'Indicator Applet Complete' (Fig.2) and 'Notification Area' (Fig.3). A logout-login should clear it (at it happened in my case) or a reboot should work as @olek mentioned.

Regarding missing icon in the panel indicator area, there is another thread with similar question. Personally, I have not seen one but I'm guessing it could be 'ayatana indicator application'. I could be wrong though.