Truecrypt & successors like Veracrypt use encrypted virtual hard disks, which are a single file that when opened by software act like a normal hard drive. Nobody remembers the names of 13k legitimate folders let alone 70k files, plus you have all the other files & folders on the system disk. The main alternative way to hide files is to hide them in plain sight - something else used by malware writers - & since the Windows folder in a fresh win10 32 bit install has ~70k files & ~13k folders, you have both opportunity & camouflage. And like the malware versions they can survive & work because most most Windows devices only have the one OS installed, & most people don't go looking, or defragging, or use CCleaner, or any of the other tools folks have mentioned that reveal hidden folders. It's sort of a reverse dual-use case that utilities that hide files &/or folders do basically the same thing, load software when Windows, starts telling Windows not to see hidden files/folders. This serves the same functions as the more serious stuff, persistence & optionally file hiding, but anything hidden is visible when the driver doesn't load, when for example you use another, clean OS to look at the drive. Thankfully most malware isn't so sophisticated, & at most adds a driver to Windows that loads when Windows starts.

This gives the malware what's called persistence - you can delete other files belonging to the malware & it always comes back - and it can tell Windows to not see specific files, & if you can't see them, neither you nor your security software can get rid of them. Malware writers came up with the trick to put files in the 1st, hidden section of the hard disk, in the bios, & in extreme cases, in hard drive firmware. The file system - ntfs with most Windows installs nowadays - uses tables that store the file name along with where all the bits & pieces of that file are located on the storage media.

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