Depending on how much you take Roberta's word vs. that of other designers writers, (and its obvious they sometimes ignored her and did their own thing, and often she had little to do with the actual stories); she apparently never intended Hagatha to be Mordack and Manannan's sister. She has stated in interviews that they aren't (or at least to her husband who passed it onto the fans) . It was Peter Spear who tied her into that grouping, and other designers that referenced said fact in later sources such as the King's Questions (although it was never mentioned in the games themselves).
But since she basically never saw them as connected, she never had any reason to go beyond the generic fairy story that wanted the series to be an homage to.
I asked Roberta [...], and sorry to admit that she said she didn't remember the Black Cloak Society. It sounds cool. Perhaps she should have taken it more seriously and featured it in other games. With respect to Hagatha [being related to Manannan and Mordack]: Roberta's answer was, "Would you like them to be related?" Then she said, "Nope, Hagatha was her own separate person."
- Ken Williams at SierraGamers (6-9-2003)
<blockquote>...one final thing: Hagatha was never part in any discussion of a Black Cloak Society.
- Roberta Williams at SierraGamers (6-9-2003)
Personally, I take the approach that the series as a whole is something designed by many (not only Roberta), in some cases invidividual games are the products of their head designer, who told created their individual views of the universe. So basically KQ1-4 represent more Roberta's influence (and are the most pure and true to her intent to create a world made of Fairy Tales). KQV was still mainly Roberta I think (although I forget who her co-writer was). KQ6 was primarily Jane Jensen's story, KQ7 was mainly Lorelei Shannon, and MOE was primarily Mark Seibert's story. Though Roberta had some hand in all the games. Peter Spear worked with individual designers (such as Jane Jensen, and Lorelei Shannon), but not necessarily Roberta in all things (although she had endorsed reading them as a way of better knowing King's Quest). It was Jane Jensen who wrote the Guidebook to Land of Green Isles, and chose to include Derek Karlavaegen when it was suggested to her. The novel series are mostly just a Sierra licensed product and Roberta had little to no direct influence on them.
So I do aknowledge that others might read "conspiracies" where Roberta never intended there to be. Especially if they delve into the material that goes beyond the games. I still thinks its important to at least understand the development history, and know that sometimes her opinions stray from other designers. A good example is that in her view King's Quest occurs on earth in our past, which is a bit different than the KQC which placed it in another universe.
"The chronicles of Daventry are retold, these centuries later, as the tales of King's Quest."-Roberta Williams, InterAction (Fall 1992)
So basically there are sometimes two parallel and official story threads going on. Depending on how purist people might be, they might side with one version over another, or try to incorporate both in some fashion. For example Jane Jensen and Lorelei Shannon incorporated King's Quest Companion details (but more or less stuck to the "Earth's past" scenario in the manuals and ingame text). Whereas Roberta might have had a different take on the universe.
But ya back to Hagatha, it seems that Peter Spear never really did much with Hagatha, other than in the KQC, 2nd Edition, which covered KQ1-5 he tied her to Mordack and Manannan, and also stated that it was possible that their evil family was possibly the cosmic balance to the royal family of Daventry, that they it was fated for one to cause evil that would affect the other, while the other was forced to stop their evil to bring things back into balance. If things swung too much into the side of good, it was the dark family's duty to balance things in the other direction. This had to do with family however (and had nothing to do with the BCS).
Back as early as the KQC, 1st Edition, which covered KQ1-4, also had a semi-evil magical guild (though not all members are necessarily evil), the Magician's Guild, which he tied Manannan and the Enchanter/Sorcerer.
http://kingsquest.wikia.com/wiki/Magician%27s_GuildThe Magician's Guild is never mentioned beyond the KQ3 material (it never shows up in most of the material relating to 4-7 as far as I remember). Though it gained at least one additional reference in the second edition, concerning the Society of Wizards.
http://kingsquest.wikia.com/wiki/Society_of_WizardsHagatha is never referenced in the KQ6 and KQ7 material in later editions. It would seem like Roberta's vision (and the vision of other authors) made Hagatha less important in the scheme of things, so too did she lose her importance in the KQ6 and KQ7 material in the companion.