exfat is also the standard for sd cards above 32gb and is what every card above 32gb I've seen has by default. saying your products support something leads people to believe it will work out of the box which they will not.
how will this make piracy easier? the only way to pirate 3ds games is with gateway which has nothing to do with this. Not sure if ninjahax emulators store on sd card but those are so small 4gb is enough.
As cia files start containing more and more content, fat32's 4gb filesize limit will become a problem for piracy.
A workaround may need to be found.
exfat would require more effort for nintendo for almost no gain, the 0.41% of consumers with large microsd cards aren't worth supporting a second filesystem for.
I'd rather them use ntfs if they were going to mess about with their filesystem support.