Well, depending on the size of the drone, you might want to limit the size of the rack you can put on there. For instance, maybe limit it to a dual rack on a Predator drone, and a Quad (or perhaps even Triple) rack on the Reaper. Save the sextuple rack for actual aircraft. But that's just how I'd do it.
Honestly, though, I don't see it being a major problem, so long as your players understand that bringing that kind of ordinance to the party WILL draw attention. Doing that in any part of the sprawl that isn't Barrens will bring the attention of not just the Knights, but also the National Guard or regular military, as well as the more elite corpsec. Even in the Barrens, it is going to get you noticed when drones start doing bombing runs with anything more powerful than a grenade launcher. However, I will admit that I've paid for a Reaper retrofitted to remove the Obsolete quality, and loaded it up with two LMGs with ExEx, a quad-rack with incendiary bombs, and a quad-rack with frag bombs. Rockets and missiles are fun, but they're damn expensive. Bombs, on the other hand, are cheap, and there are a couple good ones you can get at chargen. Most of the time, I just kept the chameleon coating going, and used the LMGs to attack. But the bombs were nice to have whenever the situation boiled down to "Pink Mohawk or die".
Remember, being Black Trenchcoat may mean that 'Wrath of a Vengeful God' isn't your Plan A, or even Plan B or C, but that doesn't mean you can't bring out the ultraviolence when stealth fails. Take James Bond. Most of the time, he is basically Black Trenchcoat (well, as black trenchcoat as a face gets). But when the chips are down, EVERYTHING goes boom.
