A lot of young children only have 1-2 games, so it's not that unlikely at all. My neices for example only have 3 games and they've had their systems for several years now.
That said, we don't know for sure what else (if anything) is logged besides the title. Is there a chance that they can look back at the logs and see more? Yes. Is it likely? Well... Nintendo probably knows what it's looking for having dealt with these carts all throughout the DS/i lifestyle... so it is at the very least possible.
The simple fact is though that no one will know for sure till the 3DS is hacked and we can fully view the logs... but again, Nintendo will never LEGALLY be able to brick your system. As long as the flash carts don't modify the 3DS firmware in any way, there is no way nintendo could accidently brick your system and any intentional attempt to do so would result in many lawsuits... both civil and federal (remote destruction of computer systems is against the law in the US, EU, and most other modern countries).