There is nothing particular about perpendicular orbits that make them more or less stable; i.e., it shouldn’t approach any of the other bodies much differently than if the orbits were coplanar. It’s far more unusual to find planets in perpendicular orbits at all, because they would have formed from the protostellar disk, which is (almost always) aligned with the parent star’s spin axis.
That being said, being found in a perpendicular orbit suggests that the system overall has some inherent instability. These planets have probably been deviated from the planar orbits by the Kozai mechanism, where interactions with other bodies in the system can alter the inclination (and other orbital elements) of the orbit. I would not be surprised if later on they find the star is in a long-period eccentric orbit with another star.
