Hi there actually hasn’t been any logic for hiding the footnotes section below the content. The plugin is setup to show the footnotes inline using the qTip Javascript plugin and append a list of the footnotes below the content.
The most recent update only checked to make sure an input value in the settings was set to get rid of a PHP notice.
If you need to remove the footnotes from the bottom of the content you should be able to place this code in your functions.php.
global $easyFootnotes;
remove_filter('the_content', array($easyFootnotes, 'easy_footnote_after_content'), 20);
Or if you’re not comfortable editing php you can add a display: none; rule to .easy-footnotes-wrapper via CSS.