On the first day of Medical Informatics school they already teach you that the recording of the absence of something is entirely different from the absence of the recording of something.
I would think that the best way to capture this in the CDM would be to add a flag column to each table. All OHDSI applications (like ATLAS) would need to take that field into account.
I’m sure there are reasons why this hasn’t been done yet, but I don’t know what they are. We certainly never had this information before in most of our databases. Administrative claims data only records things that are present, and even EHRs tend to just record things that are present (and therefore fail the first class of Medical Informatics 
) So maybe we just never had a good use case before.