I'm on 18.04 (upgraded from version 16).
After following other suggestions such as wiping the old indicator-* programs, and installing the "Kstatusnotifieritem extension", my icons returned -yay-
..but they went away every time the laptop went to lock/or was closed for awhile. Which is often.
Everything comes back, but you have to Alt+F2+R every time, which is annoying and also rearranges my bottom bar dock thing, and since I have many terminals open and arranged, you can imagine :x.
Anyway, this post seems to have fixed it.
Removing default ubuntu[email protected] from /usr/share/gnome-shell/extensions
sudo rm -r /usr/share/gnome-shell/extensions/[email protected]
I locked it with Super+L to test it - and my icons did not go away. :D