On the subject of facilities in general, I aspire to (and occasionally fail at) trying to secure them in a reasonable manner reflecting how they would be defended. What would this mean for drones?
1) In a sprawl, people are presumably allowed to own and operate drones. And the airspace itself is going to be coordinated at a higher administrative level than every 50 feet. You can't just go dropping the things because you think they are taking a peak unless they have clearly transgressed on your property and out of City airspace; and presumably have been given a few digital warnings to the ffect of "turn around, don;t be here." Think of the liability and the paperwork! That said, the average corp is going to know that. The average corp also does not have an unlimited budget so, here's a few plausible counters in that environment:
A) Reflective windows. Glass blocks thermals by default (useful bit of knowledge right there as a GM), and giving windows that sunglass mirrorshade look is both aesthetically pleasing and renders standard observation very difficult. Plus, you know, its a lot cheaper than DroneSmacker 5000.
B) Flood the EM or silence it. Either have everything, la di dad di, EVERYTHING, broadcasting in the near EM or have nothing. In the first manner, anyone doing digital snooping is going to be flooded with so many signals that its hard to pick out which is useful and which is a roomba. Sure, you're having packets get sniffed, but every one of them has some encryption on it. Give the NSA a year and maybe they'll find the key stuff y brute force, but otherwise an undirected snoop is playing the lotto to find anything more interesting than the automated coffee refill ordering. For the second, it's obvious - if no EM comes out of a building, hard to listen. The obvious mix would be to silence critical signatures while broadcatsing a ton of lfuff anyhow.
C) Tagged airspace control; local. Permitted drones all get a tag attached which broadcasts an RFID. Tags are cheap, but anything riding in your airspace without the right tag and emitting an electronic signature is not yours. Now you have legwork in the run - if you want to do drone recon in close, you gotta find bob in drone maintenance and compromise him. (Or whatever)
D) Good matrix hygiene.
I'm sure you can think of more.
2) What do you do with a wayward drone? Well, you probably don't scratch it out of hand. The people who know it is there may give it a warning depending on how legal your area is, but not before sizing it up. Get all the good signature and identifying data off of it; if you do get in, far better to stay silently in the system and find out who is running it and seeing how far back you can track that than crudely spike the thing. Even that is a lot of effort; just file it, warn the drone, and continue life. Maybe down the line someone realizes the drone with that number was reported stolen from delivery and one of the player's contacts isn't willing to deal with the PC because the cops are prying about why mosquito shipment 1234 went through his hands when ti was clearly reported stolen. Or the automated LE systems just track the NAC/SN whatever back to DroneMart, and find that a certain SIN purchased it - which gets ignore until that SIN pops up again somewhere else, then BOOM, full video, audio, etc from the store becomes the basic "who we're hunting".
Now, if a second drone comes in under the same clear control source, or the first becomes suspicious, that's when the hacking types go to work back tracking the operator. as the sec guy in that case, you don't want the far end runner going "drat, thats 300 yen", you want him going "uh huh, uh huh, looks good, yeah....guys about the second stairwell...hey, is that someone at my do---CRACK! DOWN ON THE FLOOR MOTHERF*CKER! - end signal", or, if you're playing a table where corps are less extralegal, then just know that once the second drone gets compromised, someone is going to spend a few hours counter gathering info: the warrant is ready, and the target package to send someone after the runners is all que'd up, just in case they try something. You do not need to destroy a single piece of equipment as the GM - let the players go through the joys of trying to burn an identity, at least electronically, if the rigger gets his drones found, hacked, and backtraced. Drama for all, and a reasonable and cost effective corporate deterrent.
Needless to say, even if the drone isn't cracked, once the security knows it is there, they know where it is looking. The players might just find that sewage line is no longer as easy to get in from as they thought come game day.
Or if you're in true brutal genius/zero zone mode, security lets drones penetrate into preplanned traps; make security seem hard at one place and soft at another to tempt runners in to places where they can be easily isolated and killed or captured.
3) You're not in a sprawl. You're in Chicago. This is effectively a war zone. Better hope that drone doesn't get compromised, because if it does, the timer is ticking on when a couple missiles from 30k feet up end the runners.
