I've had the same problem for a few months with missing icons in the menu bar, finder window and others. I rifled through settings of every sort in my Macbook with no resolution. After a hefty amout of interweb research, I have found that, while your third party software may be dead, the intial problem with these conditions is the latest Apple update. A temporary fix is to boot up in safe mode which will rectify the issue, then boot into normal mode. This worked for me for several days as I was careful not to let the computer go into hibernate, which is the trigger for the problems of this thread. But once I did let it hibernate, problem was right back. Nothing but empty space in my menu bar where the spotlight, battery, bluetooth, wifi, and Apple TV icons normally reside. But others like the message center icon, my name, clock, Time Machine(well the hands anyway, the circle arrow was missing), remained along with a couple third party icons for a memory monitor and a temp monitor/fan speed app. So more web research and I came to the conclusion that the update must go. So, discovering that Macbooks have the ability to restore systems files and folders over the internet without any discs and most wonderfully without losing or having to move one single piece of your info that is on it, I got busy at it. For precaution's sake, and never having used the lossless restore, I forced a Time Machine backup for the absolute latest system image, made a backup of important files on one external HD, and a redudant backup of important files on another external HD.
I then restarted, held Command "R" at the startup tone to enter restore mode, and selected the option to restore without losing files(can't recall the exact option name). I was promted to enter my password for my iTunes account so my Macbook could download various necessary files and then it began doing it's thing. The initial stage of downloading files took an hour and fifty minutes which upon completion advised of the beginning installation process which was a 32 minute deal. Once that was completed, it rebooted and I was greeted with my lock screen that was just as I'd left it incuding paswword was the same, lock screen photo was the same, and even the little profile pic was the same. I signed in expecting to spend more time downloading many of my apps, especially third party, but to my surprise everything was, as I said before, just as I left it. All of my apps were there, including third party utilities, programs like GIMP and Blender, and even Reason and Audacity were still as I'd left them. The only thing I had to download again was an updated version of iTunes, which also included updates for Safari, Aperture, and the infamous "MacBook Air and MacBook Pro Update 2.0". I selectively downloaded iTunes and the update for Safari and passed up the graphics update and the one for Aperture since I neither have or need it, nor have the cameras for which it extends functionality for Aperture. You can choose the parts of the update that you wish to download by simply going to the App Store updates section and instead of clicking "Update", click on the "...More" selection at the end of the description section. This brings up a breakdown of the update in which you can selectively choose which parts of the update to download.
Everything else in my MacBook was normal, including all of my icons returning to their rightful place of residence, and I suffered not a single loss of any info that I've found to date. I did the restore just inside of a week ago and after many hours of use and many shutdowns and many sleep and hibernate cycles, I have had no return of any of the conditions that were previously irritating me since the update was initially installed. Hopefully Apple will rectify this problem in the next update, but until then, I hope this bit of advice can help alleviate the stress for others.
