Yeah that seems completely safe. All offline games are good. All personally ripped games are good. And if the common theory is correct, .3dz games with private headers (even from different games, offline or online) are good. Public headers are risky and most likely the cause of the bans. CIAs seem safe for now, but that may change.
But if Nintendo does try to ban people with CIA files by cross checking them to see if they were bought, that would take quite a bit of effort on their part. They'd either have to have initial reason to suspect you before running the check, or do random checks periodically, or somehow check everyone who has played a 3DS game online. And they'd have to do that regularly (and we know their servers suck, that's take up a lot of resources).