Many examples have been given for both intersteller and insystem applications for astrogator. You might not like them, but they exist, and I think most people will find them compelling.A rule that has no effect on anything is a waste of space in a book where space has a cost. If you spend time explaining a limit that does not, in fact, limit anything, then it's just useless. Which is the case for the interstellar application of the rule.
For the in system application of the rule, it has the same problem with any other in system travel. There is no way for the referee or the player to actually know where two bodies are in relation to each other at the any given time that is consistent. Can I jump from Earthport to Jupiter at the moment or is the Sun's jumpshadow in the way? NO IDEA. So, again the rule becomes unplayable.
Real space has this problem, but it at least has a "take the average and then use a randomizer to determine where it falls at the moment" workaround. Jump is a yes/no question, however.
Edit: You asked how it is undesirable. I ask: how is it helpful or desirable? In what way does it add something interesting to the play of the game?
As with Gun Combat, you need to know where the target is to decide if the shooter can even shoot at the target. Does this make it impossible to use the skill? Is this a problem for the skill's very existence? In my view, it is not. The referee can decide where the target is, or figure out based on the target's last known position and movement where it is, and either using a map and checking sight lines. If theater of the mind is used, consistency might be a problem, but referees in my experience are mostly up to the challenge.
Same with jumping. I recommend just making a roll for line of sight on the first occasion, and if the issue arises again in the same system, make sure you give an answer which makes sense given the movement of the planets in-between times. If you really want to dive in, use Universe Sandbox, but for most referees, most of the time a guestimate will do the trick. Precise locations for planets can be given, if you want to go to the trouble, but 99% of the time it is just as good to wing it. This doesn't mean it is not important: if the referee rolls that you will need to fly out to get a line of sight on your target star outside jump shadow, it might be the opportunity the pirates need to jump you. It just means that an approximate answer, given on the fly, will work just as well - as with a theater of the mind gunshot, the effect is still still there. You don't need to calculate the orbital dynamics to know that planets will circle around their star quickly if they are in close, and slowly if they are out far. (and this problem is not the fault of Astrogation skill, or of jump shadows: you still have this issue if you want to fly your spaceship from one planet to another. This is a space opera type game: flying spaceships around is baked-in, and the issue of knowing where planets are arises, jump shadow or no)
Why even bother with any of this? Space travel and jump space need rules so that we know how they work in game terms, and electroplating from the basic principles is needed to apply them to specific situations. Players will try to figure out solutions to the problems you present them, and to do that they need understand how their environment works. These things add to game play because they create potential problems and strategies to solve them, and shape a terrain on which spacecraft move. Things could be done differently, such as not having jump shadows, but then that creates a whole different terrain and different set of problems and solutions, which are not developed at all in the canon.