Highly unlikely they'll ever implement NTFS. Even under Linux, NTFS drivers are reversed engineered because to get 'official' access to the NTFS specifications requires a licenses from Microsoft.
I don't think the R4 dev team is going to care about licenses when your making a product that plays pirate Nintendo DS commercial roms....that's the least of their worries!
File Systems are an essential part of any OS and without them they don't work. I can't see Microsoft issuing any law suits with regards to that.
Now if their new file system information got out, then I can see heads rolling!
My point was more the fact that there isn't any official documentation for NTFS. Even NTFS-3G, which is the most advanced open source driver still isn't feature complete, and it was only released as a stable earlier this year.
The fact is, unless an 8+TiB flashcart comes out any time soon, there really is no need for a flashcart to support anything other than FAT/FAT32.