The minor update improves system stability.
System Update version 3.0.0-6 is now available and should be delivered to 3DS systems worldwide shortly.
The updated version doesn't appear to include any major changes. Nintendo's website states simply that "further improvements to overall system stability and other minor adjustments have been made to enhance the user experience."
Nintendo has used similar language in the past while patching security holes in order to block Flash cards. Messages on various Chinese message boards indicate that this is again the case.
While the small update will be delivered automatically, users can update immediately through the unit's System Settings app.