What I do is I create the overlay/popup outside my viewport (i.e. somewhere where the camera never goes), put all the Buttons and Labels etc. on top using the Pin-Behaviour and then move it to the viewport when it is supposed to appear. That way you never have any problems that you might trigger a invisible button. As Kyatric described above, it requires some level of organisation, but it turns out to work quite well...
However, if you encounter any performance issues in your specific game and want to save ressources, try going down the road Joannesalfa described. It'll save you some GameObjects during gameplay until you really need to display them! ;-)
Just an additional idea to stay organized: You might want to put the "Popup-Events" (triggering buttons etc.) into their own group: That way you can activate and deactivate them with a single activate group action in your EventSheet.