According to jira documentation:

The "NOT IN" operator will not match a field that has no value (i.e. a field that is empty). For example, assignee not in (jack,jill) will only match issues that have an assignee and the assignee is not "jack" or "jill". To find issues that are assigned to someone other than "jack" or "jill" or are unassigned, you would need to type: assignee not in (jack,jill) or assignee is empty.

This is very frustrating, and besides that our users are not aware of this limitation (unless they dig in the doc which they never do) and thus complain that the query results are not correct.
I would also believe that a 'not in' result should return non-match AND empty values.