Apparently, a [relatively] recent change to the back-end side of Nautilus file manager, has depreciated the option to change whether Nautilus should show hidden files by default or not from its org/gnome/nautilus/preferences inside dconf editor.
This change which began from Gnome version 3.8, has caused quite a confusion for those who are used to commonly ignore the summarized description below the option itself and also for those who didn’t even knew it existed.
However, you’ll find that upon reading carefully what the description says then the answer to your problems will be magically solved (if not all your life problems, then at least that one :).
Prevent hidden files from showing by default
In order to do that, you’ll need to (install deconf editor first, then) open up dconf editor and navigate into org/gtk/settings/file-chooser, here, uncheck the show-hidden variable, then close the app.