I doubt they went with a 8GB card, especially with a limited run (less units made = more expensive). Besides, Fire Emblem Awakening is somewhere around 1GB iirc, so it'd be quite "impressive" if Fire Emblem if was bigger than 4GB in total (what's more, I presume there'll be quite a lot of shared assets between the two versions).
But yeah, the limited run (well, I say limited due to how fast it sold out, three months before release) is probably partly due to the cartridge used. My money is on 4GB, 8GB would be utterly massive (unless the game is filled with pre-rendered cutscened, uncompressed audio and voice acting, etc.), and no game has used such a cartridge before.