Today in the morning I tried to compile my project to run in my device and I found the destination toolbar disappeared and I cannot choose my IOS device or IOS Simulator dev
I came to SO looking for an answer but realized that I had seen this issue before.
So the problem is basically that auto layout sucks (I mean it is not working properly in Xcode 6) and on El Capitan, the destination toolbar is for some reason hiding instead of collapsing properly. So when your Xcode window is narrow, the destination toolbar disappears.
But, if you expand the window far enough, it shows back up again.
In case you can't tell, in the first screenshot, the window is about 1241 pixels wide and in the second screenshot the window is 1541 pixels wide.