Ok but what about all the games already sold? Will Nintendo call them back for a 'maintenance update' and send them back to users with the new autentication method enabled?
The only thing which may be useful to distinguish a real cart from a fake one is it's speed into accessing or reading rom data. Since SKY3DS emulates another device it's quite probable that it introduces some delays in the process.
Perhaps Nintendo already figured this out but I think that to mantein cartridges's cost low, manufactures use cheap memories sometimes and this usualli implies low access speeds. So we have genuine games in circulation which have slow transfer speeds and with a high probability to be detected as fake ones by a check on the speed only...