In case of Noctural, she has a thing against the guild going because Gallus was a sort of devoted knight to her. Same with the cursed cowl in Oblivion. It seems Nocturnal enjoys meddling in the affair of thieves but she's pissed when she finds a thief that's smarter than her. The Night Mother grasp on the guild is not that strong: she cannot perform any other activity than being a sort of 'answering machine' for those who try to contact the Brotherhood for a job. Astrid demonstrated that the Skyrim branch of the guild can prosper even if contracts are obtained via a more 'mundane' way. The warrior guild has no god patron. Same for the mages. Some of them may revere Julianos but gods don't interfere in Mundus as daedra do. So, not all the guild have a connection to a Daedra.
Just like the TG, the DB needs a patron diety in order to prosper. But unlike the TG, I always put the DB one notch higher. Simply because their patron was Sithis himself---father of all Aedra & Daedra. So while somewhat trivial, the Night Mothers role (as the CEO admin assistant/answering machine) always made the DB more special than the TG. Besides, the Mother provided all DB members with a direct conduit to Sithis. Unless you were a Nightingale, the average TG member only got to interact with the Nocturnal indirectly (from blessings at her shrine, orders from Brynjolf etc).
Interesting point on the Warriors Guild. I'd have agrued that Hircene would be the best Daedric Patron for that set based on the Companions questline. Or perhaps even Molag Bal.