Afaik all the stuff you can see using the "show inaccessible systems" option are systems that are either being reworked or are kept in the game files in case they are needed in the future.
One of the cool little things I noticed in the Omicron Pi systems is that when you click on the Collapsed Jump Holes, it tells you what systems they used to be to.
Sure would be nice to have that for the others too. I remember systems like Omega-58 I used to go through years back but I dont remember what systems linked to them anymore, but I am betting the old jump holes are still there.