Hello, and thank you for the interest! You probably hit the sim max; there's a point where sims will start getting culled just to make sure the game runs well, and then the sims are effectively deleted from the save. I know that setting some sims to never be culled with MCCC works since I've done that with like.. 100 sims from my legacy? But if you try that for every single sim in the save I think things start going wrong above 800 or so, and they'll get culled anyway. To answer your questions (...might be a little disappointing, sorry):
1) The .json files part of my mod is basically a preventative measure to keep a bit of sim info and parent relations before sims get culled - so the only way to get the information back is by going to a previous save, writing these sims/relations to the .json file, and then loading these in your current save. I had previous versions sitting around from the times that I've backed up my saves+mods before big patches, so I just used those. It only keeps a little bit of info (for sims it keeps their ID, name, gender, whether they have been culled, and the time they were saved; for relations it just keeps parents) since I was just thinking about what would be needed to keep track of relationships. The commands for getting parents/ancestors just get information that is available (iterating up with the parent relbit if using ingame rels or parent lists if using .json files) rather than recovering lost info.
2) Sadly, you will still get greyed out sims if they get culled. I have no idea how to have those sims and connections still show up in the family tree UI if the sims have been deleted. I've been looking into the code and it's fairly confusing - sometimes relations show up that no longer exist in the game?? So I'm guessing it's a completely separate system from relationship bits, and I can't find any documentation for working with it. I'd like to make the backed up family info more visual at some point, but atm connections from the .json files only really work for giving the relation between two sims ingame.
3) You can safely delete the mod with no difference to your family tree in the game - it just means that any family info you've saved outside of the game (using the mod) won't be usable, and you can't find distant family relations without clicking through the family tree and working it out yourself.
I hope that helps! But yeah, that feature is more of a workaround to keep relations even if sims are culled later, rather than preventing culling (which destroys performance) or un-culling sims (which afaik is impossible).