The use of dark side allies such as the Inquisitors and the Nightsisters was not a violation of the Rule of Two since they were not considered Sith. The distinction between a Sith and a mere dark side ally is important because the Sith had secrets which they did not share with other dark side users. For example, there was a Sith shrine below the Jedi Temple which "even the most powerful of Dark Side Adepts" did not know about:
The two of them were in Sidious’s lair, a small rock-walled enclosure beneath the deepest of the Palace’s several sublevels that had once been an ancient Sith shrine. That the Jedi had raised their Temple over the shrine had for a thousand years been one of the most closely guarded secrets of those Sith Lords who had perpetuated and implemented the revenge strategy of the Jedi Order’s founders. Even the most powerful of Dark Side Adepts believed that shrines of the sort existed only on Sith worlds remote from Coruscant, and even the most powerful of the Jedi believed that the power inherent in the shrine had been neutralized and successfully capped. In truth, that power had seeped upward and outward since its entombment, infiltrating the hallways and rooms above, and weakening the Jedi Order much as the Sith Masters themselves had secretly infiltrated the corridors of political power and toppled the Republic.
Save for Sidious, no sentient being in close to five thousand years had set foot in the shrine. The room’s excavation and restoration had been carried out by machines under the supervision of 11-4D. Even Vader was unaware of the shrine’s existence. But it was here that they would one day work together the way Sidious and Plagueis had to coax from the dark side its final secrets. In the intervening years he had actually come to appreciate Plagueis for the planner and prophet he had been. Such perilous machinations required two Sith, one to serve as bait for the dark side, the other to be the vessel. Success would grant them the power to harness the full powers of the dark side, and allow them to rule for ten thousand years.
Tarkin, p. 101
There were still only two Sith -- Sidious and Vader -- so the Rule of Two was followed.
That said, the use of dark side allies could be considered a violation of the spirit of the Rule of Two. The Rule of Two required the Sith apprentice to defeat the Master in a one on one duel to ensure that each new Sith Master was stronger than his predecessor. The Rule of Two also prevented the Sith from fighting each other for greater power instead of their light side enemies (though this was less of a problem for Sidious and Vader with the Jedi Order almost entirely eradicated). Without the Rule of Two, a group of Sith apprentices could band together and overthrow the Sith Master by sheer numbers -- if that happened, the new Sith Master would be weaker than his predecessor. By using dark side allies such as the Inquisitors, there was theoretically a danger that Vader and the Inquisitors could band together and defeat Sidious -- Vader would become a new Sith Master but would have been weaker than Sidious. This would have been an unlikely event, though, and in the end that particular threat did not materialize.