Okay, as John pointed out in the comments, my "Deep Cover, Deep Magic" post ended up pretty much describing the premise of White Wolf's Mage: the Ascension RPG, in which a secret war is being fought between wizards and the Technocracy (and others) for control of the nature of reality itself. Oops, I forgot about that. Well, that's not quite what I was thinking of, in any case. Because in all this talk about powerful wizards and Deep Magic, I sort of forgot about the Deep Cover part -- as I said at the beginning, it's not just "magic-powered espionage."
As Steven Brust wrote, "No matter how subtle the wizard, a knife between the shoulder blades will seriously cramp his style." Or a high-velocity round, for that matter. And that's where Spycraft comes back into the game. No doubt some of that comes up in Mage:tA as well, since the Technocracy, being the forces of science and technology, would hunt their foes the mages with "mundane" weaponry. (Note that I don't know a lot about Mage:tA, so this isn't necessarily wholly accurate.) But I'm thinking more of a struggle among powerful mages in our world, where super-spies and high-tech assassins are just more tools in the arsenal each mage can employ. Just because you can blast your foe with a Fireball doesn't mean that's always the best tool to use.
And to complicate things further, sometimes, the best way to hide something is in plain sight, and that is as true for wizards as anything else. After all, having mighty supernatural powers at your command must at least sometimes make it easier to gain power in the mundane world, even if you have to hide your magic from most regular people. So when your PC superspy agent is sent out to eliminate Presto the Magnificent, he's going to find it much harder if Presto is also Thomas Smith, CEO of TechCorp -- or General Smith of the Joint Chiefs of Staff -- or Cardinal Smith, the Pope's closest advisor. Fortunately, those charms your employer gave you will hide you and protect you from the vengeful wrath and powerful magic of Presto's lieutenants -- won't they?