Apple - Icons disappearing from menu bar

Although I do not know the problem, there are several solutions.

1. Reboot or Log out.
2. Kill the SystemUIServer process, either via Activity Monitor or via killall SystemUIServer. The UI server will restart and the problem will be gone. I've seen it happen that I needed to kill it twice to fully take effect.

I thought I'd add that I had this issue again in Yosemite 10.10.3. A disk repair, 10.10.3 download & reinstall, deleting SystemUI preferences .plist, etc. had no effect for me.

What did work is a simple Safe Mode boot. No actual changes in Safe Mode, simply booting into it fixed my system menu bar icons. A reboot back into normal mode still had them fixed.

You can access Safe Mode by holding Shift right after the chime during startup.