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afaik Horde Battles pull from the Pokémon available under the current conditions. Just a guess on my part, but I could imagine that for this purpose the "rarity" value is ignored - so if you just set their rarities to 0 to disable spawns, that might still be recognized as a viable spawn for Horde Battles.
You can instead override theirrespective spawn sets with an empty file in your Data Pack, which will make it so the game can't find any spawn details for them at all.
If I have to, I will delete their spawn .jsons entirely. Will deleting the spawn files prevent them from being in the game? As in they couldn't even be added with the PokeEditor?
If you mean you changed the files in the actual mod JAR itself, please don't. Modifying the mod itself can cause issues that are next to impossible to provide support for. These customizations are explicitly what the Data Pack system exists for: https://pixelmonmod.com/wiki/Datapack_Creation
As for making them impossible to obtain even with cheats, for that you'd have to override their species files under "data/pixelmon/species/" with blank ones. You may also have to modify or remove any and all data files that reference those species to avoid issues from the game looking for species that don't exist though. I'd recommend against that, because there may be hardcoded cases which you can't override.
You could however add the "undexable" tag to their species files (as used in unfinished species like Iron Treads currently). With that they won't be needed for Pokédex completion anymore.