Per ICD-9-CM coding guidelines, "Assign codes from category 403, Hypertensive chronic kidney disease, when conditions classified to categories 585 are present. Unlike hypertension with heart disease, ICD-9-CM presumes a cause-and-effect relationship and classifies chronic kidney disease (CKD) with hypertension as hypertensive chronic kidney disease."
Tabular list section for 403 code range includes an exclusion noted stating, "excludes renal disease stated as not due to hypertension." So, the only time you do not link them is when it is specifically stated that they are not linked.
Your codes for the hypertension and ckd would be 403.90, 585.4, and V45.73.
Hope this helps.