If the shadow is in the destination system, won't help. And, travelling up/down doesn't matter. It is the added time doing so that matters.
The shadow is 3D not 2D.
So, have the astrogator plot a jump course that goes above or below the shadow of the Primary. Yes, you'll end up further North/South of the mainworld than 100D due to trying to go above or below the System Primary 100D but surely a lot of the time that would be the closest approach than ending a jump anywhere else in the system because of a Jump Shadow, unless the mainworld was on the edge of the Primary's Jump Shadow. And yea, for simplicity sake assume that most systems have planetary orbits in the galactic plane. Once a system is completely surveyed by the IISS then the orbital period and paths of each world in the systems would surely be part of the standard navigational data. Jumping into a system North or South would also avoid any Jump Shadows of any GGs, provided their orbital paths are in the same plane.