There might be an option to show them, not sure.
i use cuteftp 8 pro and they show up in the help here's how it says to show hidden files
To see hidden files on a remote site
Select the Site Manager tab.
Select the site with the hidden files.
Choose File > Properties from the menu.
Select the Actions tab.
Select Filter.
Select Enable filtering.
Select Enable server side filtering.
Enter -a in the Remote field.
Select OK.
Connect to your site.
Bookmarks