How so? Commercial roms have indeed reached 128 Megabytes in size. The whole megabit-vs-megabyte thing was mostly used in the GBA era.
And official games contain a built-in filesystem that reads and writes parts of the game into RAM as necessary. Homebrew must load a <4 MB file first into RAM, which can then access the larger files on the media card. It cannot however load a 100 MB .nds file.
Surely you aren't suggesting that the DS loads the entirety of the FFDS game into RAM to begin with, right? Official games and homebrew games run in a similar fashion, but one simply has the filesystem embedded into a single file, we must use external files to accomplish the same task.