App icons disappear from home screen on app update
This is not a bug with the Nexus 5.  It seems like the Google Experience Launcher (aka Google Now Launcher) seems to handle app shortcuts a little differently than other launchers do.  The cause of this has to do with the way the developer is updating their app.  I have seen this problems specifically with Franco Kernel Updater on my Nexus 5 with GEL/GNL, almost every update that comes out I have to add the icon back onto my launcher home screen.

I think I read somewhere that it is when the manifest file is changed... but don't quote me on that yet.