I am not quite sure what you mean by "media folder". No. There is nothing about mounting other drives that requires that the data acually be copied to the Linux partition.
Most music/video apps have some kind of option to copy files added to their own library which sounds like what might be happening to you. So you might check to see if those programs are set to do this.
I am guessing that the Windows partition is NTFS which can be mounted, but only in read-only mode. So your media player apps might need to copy them over so they can have full read write access. There are usually fewer headaches mounting windows partitions when they are setup as FAT32 instead of NTFS.
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