Nope.
Non exist.
Cant say there havent been any attempts at all though, but I cant say even that as I really have no idea.
So in otherwords definitly not.
Though a nice NDS listing program with file extracting to USB drive (DS-X) would be a cool addition to rom organizing applications.
GBA flash carts are all differnt in one way or another and would be too hard to make and flash correctly for all of em.
So best bet is to do it the hard way.
Organize, then grab the files and burn em manualy. Or make copies and delete them later and jsut keep the organized ones where they are.
Though an NDS prog with small little file "send to" routines would be great xD
I should code one >.> (after learning C++ once and for all)