The minor update improves system stability.
http://www.nintendoworldreport.com/news/28765
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.
Since the last update I've had my 3DS refuse to come out of sleep mode when I open it a few times, forcing me to do a hard reboot. Hopefully this fixes that.Mine did that. Then it would let out a high pitch squeal when it went into Sleep sometime and eventually blue screening. Literally Blue Screening with the dump numbers and everything. I had to send it into Nintendo and they unfortunately had to send me a new unit so I lost all my Street Pass and Coins things.