First, not gigabytes but just about 200-500MB. (I'm writing this app for fun and to learn Java, so this is a very optimistic estimation of dictionary completeness.) I don't think that database size will exceed 2GB. (This is maximal file size for FAT16, as far as I know.) Any modern file system (NTFS, ext4) supports 2GB+ large files.

I believe a single file database is less confusing for a user. Even Java DB now supports archived databases, but unfortunately only for reading.