Both FAT and NitroFS are automatically supported by the libraries that PokeDS is built upon. NitroFS is a file system that is tagged onto the end of the .nds ROM file therefore allowing you to circumvent the 4mb resource limit. (PokeDS is already nearly 1MB, NitroFS will be very useful). I haven't looked into it but I'm fairly certain we will be able to copy files directly into the NitroFS making things like files lying around on the FAT which may be prone to user modification non-existant. However, the support for loading files from the FAT is definitely there and is easily used.
Looks like I was wrong! NitroFS has no write permissions once it is baked into the ROM.