Why Are My Cache Files & Other "Hidden" Files/Folders Visible? & How Do I Get Rid Of Them?

I hid mach_kernel and private, but the cache.db, cache.db-shm, cache.db-wal of both the system and user folder are, also, visible. Yesterday, I had to restore from a Time Machine backup because something had suddenly eaten all the space on my startup drive. However, these files were visible prior to the restore. So, why are they there and how do I safely dispose of them or hide them to prevent their return to visibility? Thanks.

Applications/Utilities/Terminal command.
defaults write com.apple.finder AppleShowAllFiles FALSE &ampo; killall Finder

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