The impression I got from Filloni at the time is that those killed in 'Twilight of the Apprentice' were meant to be the last ones left.
I don't really buy Palpatine and/or Vader just killing them because they're a threat. Let's be honest; none of them were ever a threat to either Sidious or Vader, nor would any of them make particularly formidable Sith apprentices. Indeed, that's kind of the point of them. Competent enough to be useful, not competent enough to be dangerous.
Also let's not forget that in TCW Sidious abducts force sensitive younglings with the intent of creating a network of brainwashing force sensitive spies throughout the galaxy. That clearly doesn't describe the Inquisitorious, and we know the collection of younglings continued under the Empire, so it's a fair bet that Sidious had a parallel program running, and I wouldn't be surprised if at least some of the Inquisitors were rejects from that program. What could have become of that network after Palpatine after his "death" is a bit of a mystery, though one that might factor into whatever Thrawn is up to post RotJ, or eventually come back in some eventual post tROS stories. Or I guess they could all have automatically terminated as part of Operation Cinder. We'll see.
