What's the difference between cloning a hard drive and copying all the data (files and folders) from one drive to another? Is there invisible system data that you can't transfer?

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Several differences:

• cloning copies the complete layout of the disk, including physical location of all directories and files. At least some older windows versions would not run without specific files being in specific (physical) places.
• cloning copies also content of deleted (and 'non-existant') files
• cloning copies also the partition table, and potential hidden or unaccessible OS partitions. Those are required to run, at least for Windows 10.
• cloning is typically faster, as it doesn't need to care about directory structure, file structure, fragmentation, etc.
• most important: if you are copying the current operating system disk, a lot of files are locked, and cannot be copied. You will not be able to run the copy of most OS.

If you are not copying the current OS disk, but only data: only the speed is relevant - coying is still much slower.

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