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Mods can however add more squads to the world, but if you especially went under the Nameless folder when save editing and all 1000 squads were under there....
Your characters should be in the oldest/first squad.
It is a predicament rarely seen, if ever, so I am not sure how that can be fixed, apart from starting a totally new game. What you could do, if you are able, to visit a plastic surgeon and export each character bod2 file. Then you could take a screenshot of each character gear and stats and make yourself a start mod that adds those characters as start characters with the gear and stats and enough money to cover what you had possibly built and all the research (including default start) your faction had already completed.
And maybe turn the auto clicker off XD
https://gtm.steamproxy.vip/sharedfiles/filedetails/?id=1173940466
This mod for example sends raids to your base using squads of your own faction, they spawn empty but still show up i the squad list, and have their AI attached. If you have that mod or similar and just left it on and running it could generate tons of empty squads over time.
Otherwise no clue, very odd issue. Do you maybe have an unusual faction name? An odd name could lead to unusual issues with it saving the squad data.