If you copy an entire directory (folder) to another
location, do the hidden files not move unless they were
visible at the time of copy? I realize that moving into
the directory/folder and selecting all files will select
only the visible ones and thus Ctrl-C will copy only
those to the buffer. But from outside the directory,
won't the entire folder be duplicated no matter whether
the files inside were visible?

If you grab the folder icon it will take all files in it, including hidden files
and folders. However, if you select folders within the folder they need to be
visible so that they can be selected. Otherwise they will be passed over and you
will only get the ones that you can see. So that makes you correct and this
would have been another way of doing it.

However, when they copy back they would not want the user folder, just the
contents, so to keep it simple and consistent, I opted for that method. I tend
towards keeping things parallel when possible when dealing with new users. I
also tend towards giving graphical solutions rather than commandline ones for
the same reason, simplicity.