I think everyone is panicking at nothing. At best, this is a garbled translation by the manager of a single retail store.
My guess is that while the 3DS will log activity on your system, Nintendo will never actively brick systems remotely. That violates various consumer rights laws and will only lead to bad publicity and class action lawsuits without helping the bottom line. Disabling a CE device you paid money for is akin to vandalism - it'll never happen.
However, if you do soft-mod your system somehow, it means that if you try to update in future, the system will be different to what the update is expecting. Sometimes, this will mean that the update won't install correctly and introduce bugs - resulting in a brick. If you tried to sell the system back to a retailer and they could tell (via the log) that you soft-modded it or violated some higher level system permission, they then have every right to refuse to buy it from you since you modded the system. After that point, they have no guarantee that it will work as intended and have a duty of care to not sell a potentially defective unit on to other customers
If you mod a system or otherwise do something to it that allows it to do things it wasn't designed for, that's the same as spray painting it or putting sticker decals all over it. You wouldn't expect to be able to take it back to the store for a refund or to get a good trade-in price for it if it isn't close to the same condition as you bought it in. This has nothing to do with Nintendo having a killswitch they can trip. Regardless of how much they might want to do it, it would be breaking the law.