From the FAQ:
Q: Is it possible to install Game Updates (and does it requires to be on the latest firmware)?
A: Yes, you can install game and system updates. The game updates can be applied following Nintendo's usual rules, which sometimes requires you to be on the latest or a higher firmware than your console's current firmware.
I don't like the fact that the team responsible for SX OS clearly has no clue regarding the matter. People obviously get banned by doing this and some don't. They don't even mention "at your own risk", they do however regarding online play (which is more common sense).
People get banned while taking all precautions, mainly updating through OFW, never touching devmenu/layeredFS/installing .NSP's and only updating games which aren't trimmed.
Some argue that Nintendon't check the certificate/header for games when updating.. if that were true, people shouldn't get banned just by updating.
It’s hardly their fault if people get banned. Nobody knows exactly what Ninty logs, so they can’t guarantee people safety. You hack and get banned, it’s your fault