It should be noted that the Clans station marines and put guns on everything, seemingly, or so its been noted by many observers. I think the notion that our view of them is an IC one, tainted by the IC notion of their inferiority, but one that offers little concrete information and leaves a lot open. Its not hard to imagine the Clans don't know the extent simply because they don't care enough to track it. Would warriors even notice if the odd merchant ship went missing? Maybe some would, and maybe that's why they have to put warriors on every one to keep track of them. But its also possible that its because the Dark Caste pray on them at least some of the time.
I think its a clear case of "what ever works for you." In as much as the Dark Caste is definatly not such a big or well organized group that the Clans feel legitimately threatened by it, it seems to be substantial enough that they don't or can't simply ignore it, so any place inbetween is perfictly workable within what's known about them in the limited information we're given.
That said, I'd probably ignore the Mongeese, who seem to have gone down swinging, and went down so long ago that there's little hope of having kept their identity after all this while. The Coyote reving, the Hellion's mini-civil war, even the Smyth-Jewel annihlation would be better candidates, though there's little to no evidance that any of these groups produced survivors that fled the Clans. And of course there's always Wolverine fragments, since we know they didn't all make it to Terra and ComStar. Add in the odd star or trinary that 'pulled a Burrock' and just up and left on their own, for no better reason than that they were fed up. Plus, innumerable test downs and lower castemen, who have ample reason to be bitter, and its easy enough to have as many or as few Dark Caste as you'd like. And with raided equipment, as well or as poorly armed as you'd like (if IS pirates can capture Clan omnis, then the Dark Caste should have no problem).