When entering cPanel's File Manager a dialog box normally appears allowing you to choose to "Show hidden files".
It is likely that at some point during File Manager, you chose to "Skip this question, and always open this directory whenever you open File Manager." if it does not appear.
To fix this in x3 theme:
Click on “reset all interface settings” at the bottom of your main cPanel screen and try to open your file manager once again
To fix this in Paper Lantern:
In cPanel, at the top right, click your username and then click "Reset Page Settings"
