How can I hide hidden files and directories in pop-up file explorer when uploading a file via web browsers, e.g. when inserting an email attachment? I checked Firefox 42.0 and Chrome 46.0 on x64 Ubuntu GNOME 15.10; both show hidden items. In this screen-shot I wanted to do a Google image search. And yes, nautilus does not show hidden files when I do day-to-day directory navigation.
A shortcut key to show/hide hidden 'dot' folders is: Ctrl+H.
This key is part of Nautilus and such (also GNOME I think) to toggle the displaying of hidden files and folders. Try that shortcut key in that window, see if that helps.
Right click anywhere in the pop-up file explorer and untick "Show Hidden Files". Poof! It's gone!