Perhaps whatever it was actually penetrated the atmoshpere at the pole. There must be objects moving in orbits that are not along the plane of the ecliptic.
It's possible. The Schumaker comet that hit Jupiter struck around a high latitude. Jupiter swallowed that without a trace in a couple days, so, if this hot spot on Saturn is due to something like that, it would have to have been fairly massive. Perhaps it is more like those stellar objects with an x-ray beam coming out of the poles, a quasar kind of reaction.