The NTFS-3G file system driver has mount options that let you show/hide files with the "system" or "hidden" file attributes. Windows uses these flags to hide files in its file manager by default. The mount options are
show_sys_files (the default is to hide them) and
hide_hid_files (the default is to show them)
respectively.
The NTFS-3G manual says about them:
show_sys_files – Show the metafiles in directory listings. Otherwise the default behaviour is to hide the metafiles, which are special files used to store the NTFS structure. Please note that even when this option is specified, $MFT may not be visible due to a glibc bug. Furthermore, irrespectively of show_sys_files, all files are accessible by name, for example you can always do ls -l '$UpCase'.
hide_hid_files – Hide the hidden files and directories in directory listings, the hidden files and directories being the ones whose NTFS attribute have the hidden flag set. The hidden files will not be selected when using wildcards in commands, but all files and directories remain accessible by full name, for example you can always display the Windows trash bin directory by: ls -ld '$RECYCLE.BIN'.