Well, as of now, there doesn't seem to be too much piracy going on with the 3DS and Wii U but if it were just that, they wouldn't have to be worried. I mean Sky and Gateway cards on the 3DS aren't as popular as similar cards on the DS, and so far homebrew is just that, homebrew, meaning so far only a few people can play backups or such on Ninjhax/Ironhax/Tubehax.
However, I believe they should still worry, this due to the very limited success of Wii U. They already lost alot of money on this, and as such I don't think they'd want to lose more on piracy.
For now, they shouldn't be worried about the WiiU when it comes to piracy, the only possible exploit hackers found was by using the Web browser (Seriously, Nintendo has a problem when it comes to securing their Internet Browser), and only allow homebrews (very limited). And, it's not even a kernel exploit and it's unstable.
As for the 3DS, just as you pointed out, there's already two flashcards available, and luckily enough, one is blocked by FW updates, and some games (apparently) like AC Happy Home Designer won't work on the second (Exploiting specific system calls to detect if it's a legit copy is a nice move).
For Ninjhax, it only applies to those who have an older version, and who also have a specific system version. Ninjhax 2 (IHax/THax) doesn't allow piracy, because it cannot access the AM service used to install games (smart move on Smealum's part), and it's likely to never enable access to it anyway (AM requires Kernel Access).
Finally, to conclude, I'd also like to point out the fact that there are two types of people pirating games: there are those who pirate them to "test" them (and eventually, if they like it, they buy it.), and those who pirate games just because *insert reason here*.
But, as many people on gaming boards noticed, it doesn't really hurt sales (unless if said person was about to buy it and decide not to be honest), since, most of the time, pirated games weren't going to be bought by the pirate.