I'm running Yosemite 10.10.1 on a MacBook Air (early 2014), and I'm not seeing some icons on menu bar and folder and on browsers too. I have been trying to look for what's wrong on System Preferences, but I can't seem to find the answers! I attached the images to make it more clear.
To boot up in safe mode you can hold down the shift key when restarting.
I would go to the Finder and open any window and right click or control click in the gray part of title bar. See what your settings are set to.
There is also a new update to the system 10.10.2 that was just released. Maybe this will fix it, along with a bunch of other problems we have all been having with Yosemite. (I hope! :).
As far as the menu icons, I know that some of the system settings as in airplay there is a button that says "Show mirroring options in the menu bar when available" and there are more I am sure.
Good luck my friend.