dmetzacher:

I thought that maybe there were some invisible files or folders at the root of the "Macintosh HD" drive that would be missed when copying things back.

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Yes, you will lose the desktop files which apply file type associations. For a big disk with a varied application set (a Quadra or PowerMac used as primary work computer), this would be painful but not critical. For a small disk and a modest configuration, you may not even notice any difference.

Unix-like systems use hidden files for commonplace functions (eg .profile). That is not the case for classic Mac OS which only uses hidden files for super-system functionality. A few applications use hidden files for settings but these will be nested away in the System Folder or application directories and any file copier (including the Finder) will capture them.

If you want to look for hidden files, there are a bazillion utilities. My favourite for System 6 would be DiskTop (commercial). ResEdit can browse a disk to view them but it is not a tool that I would recommend.