No, you won't be able to use the money, not now nor in future.
Only if u update u can use the money, but then you lose the way to playpirated gamesbackup copies on ur 3DS.
Serious talk though, as it stands today, you need two 3DS's to comfortably play backups and play online, sorry.
Play pirated games on ur 3DS!
when in Gateway Mode you have no Internet features
out of gateway mode you will be promted for a update