To understand the Ebon Magistrate, you have to understand the Magistracy Intelligence Ministry as well.
Its not just the EM that have been surprisingly effective and well funded, its been the entire MIM that's been surprising effective and well funded. I think Guide to Covert Ops (Ug) even mentions teams acting in the Draconis Combine.
The Ebon Magistrate is a secretive branch of the MIM that operates in cells, and may be outside the normal MIM chain of command as well, answering directly to the Magestrix. They supposedly have few family ties, and can be trained in anything from unarmed combat to BattleMech combat (and possibly a little of all of the above).
The big thing that sets them apart however is their use of cybernetics. Its only hinted at in IC writeups, but OOC writeups and other storylines confirm it.
Which is where the questions really begin to start. Did the Magistracy know about the MD, and did they create something specifically to fight it? Did they decide to create it simply because their allies, the CapCon, had developed some of the useful cybernetics (like dermal armor) and the Magistracy decided that they could make use of it as well with their advanced medical technology (and or a history of using non-combat cybernetics that let them adapt to the use of combat cybernetics easier)? Is it something else (one of the ISP books links the Ebon Magistrate with the Genecaste of all things)?
I mean, if you were told your allies the CapCons were experimenting with Death Commandos with cybernetic armor and possibly weaponry, you might consider the same thing.
So at its core, the Ebon Magistrate is simply a covert Operations group that uses cybernetics to do their job better.
Why exactly they were created when the Magistracy Intelligence Ministry already had an Active Response Corps is what isn't known exactly.
The Ebon Magistrate may have been around for centuries. They were so good, that no one noticed that they existed until the 3060s.
Well, I suppose that's theoretically possible, but most of the source data seems to indicate a more modern, 3050s-3060's creation. But anything is possible.
And of course, the possible biggest herring of them all is that "Ebon" was one of the Wolverine bloodnames, IIRC.