Well it also would be something like 25 to 30 years between the CW and the first EU appearance of Dathomir. In that time the Nightwitches of the CW were more or less wiped out and eventually the Empire occupied and later blockaded the planet. Even later placing it under artificial darkness. Most of the characters we encountered in the novel seem to be roughly Luke and Leia's age, so they were born during or after the CW. The shakeup post-defeat of the Nightsisters could easily shift that balance to what we see later on in he EU.
Also it could be on the opposite side of the planet. The Nightsisters and Nightbrothers being more or less wiped out by the Sith Lords (via the Seperatists first, and the Empire for any post-Clone Wars clean up operations).
Also it could be on the opposite side of the planet. The Nightsisters and Nightbrothers being more or less wiped out by the Sith Lords (via the Seperatists first, and the Empire for any post-Clone Wars clean up operations).