It's not NTFS, per se, it's the mechanism used to generate legacy 8.3 filenames that slows things down. If you know you're going to have folders containing more than about 300,000 files (and you aren't relying on 8.3 filenames) then it's recommended to
turn off 8.3 filename generation(see:
http://technet.microsoft.com/en-us/library/bb457112.aspx - scroll down to Optimizing NTFS Performance).
You can turn off short filename generation by using the command: fsutil behavior set disable8dot3