is the archaeological record also being 100% monitored and controlled?
No.
Or has it just been deleted?
Yes. That's what "With a few of the more twisted of SCP-1000's devices, we (…) reduced everything to slurry and dust that washed or blew away in spring rain and wind (…) We left no traces" means. Everything is gone. Everything. Even the things that you wouldn't have thought could be made to disappear. Those are gone too.
Everything.
Remember, the archaeological/paleontological record is very fragmentary.
