The Black Cloak Society is mentioned several times in KQ6 as such;
1. During the oracle prophecy. Somewhat cryptically.
2. During Alhazred's letter to Shadrack, you eavesdrop on.
3. On a letter discovered written by Shadrack, contains several mentions, and related correspondence going back several months to years in the chest.
4. A bunch of black cloaks are seen in Alhazred's closet/armoir, and on a hook in his study.
5. The Genie wears the black cloaks at least two of his guises, one of the more important of these guises as the evil old man that spies on you in the shops in town, and in which you trick into thinking Alexander died.
6. Indirectly, both Cassima and Saladin comment on the letter. The letter can also be clicked on a couple of other characters for some 'narrative' comments as well in the end game, IIRC as well.
There might be a reference, albeit somewhat more indirectly when you speak to the ghosts of the king and queen.
In no way did that mentions connect all the baddies from the entire series... At the most it connected Shadrack, Abdul Alhazred, the Genie, and Mordack.
KQ5 connected Mordack, Manannan and the Vizier, but not necessarily to the Black Cloaks. KQ5 only briefly discussed Vizier and Mordack's plans for Cassima.
In no way did KQ6 imply that Shadrack was the leader of the Black Cloaks. The actual hiearchy is not really known.
So while the fan games and other fan fiction 'went' off of these references... They actually embellished on the reference way beyond anything the canon games did themselves... By basically pulling in every one from Hagatha, Manannan, Lolotte and Malicia. In some cases Dahlia, and Lucreto into the membership of the Black Cloaks... and/or creating new members or leaders, I.E. Caldaur and Morgeillen, Valanice, Alexander and Pandora. These aren't just embellishments but the basis for entire central plot lines in the fan stories... The funny thing is that fan interpretations of the Black Cloaks all share much of the same ideas in alot of ways... Usually some prophecy tied to the black cloaks and the royal family through its lineage... Sometimes these prophecies are 1000 years in the making... They both concern or usually concern some ancient artifact that villains are after, that will give them ultimate power... They both involve some plot line of the Black Cloaks manipulating the magic mirror to draw Graham to Kolyma in order to manipulate his life...
Scratch that its really the plot line of saturday morning cartoons, the Scooby Doo/Superfriends, 'Legion of Doom' type plots... All pretty cliched... That's not to say even the canon games are filled with cliches themselves (they are based directly off fairy tales are they not?)... But sometimes it seems the fan stories are even more so....