Nintendo’s concern internally is that allowing consumers to attach large external drives to the Dock will cause players to see the system as less inherently portable, harming their core branding for the system as a portable home console.
Additionally, Nintendo want to ensure that players can at any time disconnect the handheld from the dock without having to wait for games, save data or other information to sync first. Nintendo’s solution to this is to only allow data to be stored on the handheld, so that any time you disconnect the handheld all the same data is available to the player.