Yeah, the extra dat files track positions of things like villages, monuments, etc. If you nuke it, it should cause new ones to be generated in new chunks, but any special effects around existing locations will hypothetically cease. Guardians won't spawn at and patrol an area if the monument data is gone. Villagers won't congregate and breed if their village data is gone, but there might be a special case for them magically designating a new area as a "village".
You can look inside the files with apps like NBTExplorer, but doing a massive search-and-destroy while preserving specific entities would require writing a small custom program. Not rocket science, but it's something to consider.
Some documented examples of these files:
…but now that I read that second link, I see:
This format is no longer used in 1.13. They are no longer seperate files from chunks, and instead included in chunk files/format.
…which means that although my concerns were valid for previous versions
, maybe they're not any more?
This warrants some more investigation on my part!