Given Nintendo's last lawsuit related to patents took several years and ended not with a court win or the game ever shut down during that time but with them getting a settlement, Pocketpair is likely fine.

Pocketpair might have difficulties partnering with many businesses even outside of gaming in the future, since I've been led to believe the non-legal effects tend to matter quite a bit in Japan as well, but they have global appeal and can find foreign partners if they need to.