The systems that are out of range are placed according to the actual location in the HIP catalogue, it makes sense, stars are easier to spot above and below the plane of the galaxy because of fewer intervening clouds of dust. So these stars in real life are actually where they have been placed in the ED galaxy. Talking of clouds of dust I will show you what I mean with my current slice 3;
As you can see right through the middle is an empty gap where the intervening matter and dust clouds make it hard to see and measure the distance and location of stars, so stars above and below the plane are much easier to see and measure so we get a much larger proportion of distant stars in high and low positions in the real world catalogues, and since the ED galaxy is built on a theoretical model of the galaxy (which is already demonstrated to be wrong in some areas) real world stars aren't going to conform to that model but will sometimes fall outside any possible location in the ED galaxy for procedural generation, making them out of range of any of our current ships.
Oh yes, as far as stars that aren't in the game at all, updates to the catalogue, new observations with new technology, show that some of these stars aren't individual stars at all, but one in a set of binary or more star systems, it's quite possible to come across stars A and B in a binary set that have two different HIP allocations to them, so they may be there, but just as part of a multi-star system.