"Bannerbomb3" is referring to an exploit in their system settings which allowed for custom firmware to be installed on the device. So fixing the bug which allowed the exploit is what is considered to have "blocked Bannerbomb3".
Personally, I think it's rather likely that Nintendo did this specifically to prevent their customers from installing custom firmware on devices they purchased, rather than because Nintendo wanted to fix a bug for any sort of perfectionist or altruistic ("user security") reasons. It can just be dressed up as a security issue, so that's what they do if they feel the need to justify it at all.
Personally, I think it's rather likely that Nintendo did this specifically to prevent their customers from installing custom firmware on devices they purchased, rather than because Nintendo wanted to fix a bug for any sort of perfectionist or altruistic ("user security") reasons. It can just be dressed up as a security issue, so that's what they do if they feel the need to justify it at all.