First, one would have to figure out if you can connect yourself through to the hostile drone. Let's take the example you list before you:
Steel Lynx has orders to shoot at anything in the vicinity. The SL is not on a network and is only working off of it's dog brain and it's IFF sensors. Since I doubt that it has an agent or sprite running inside, let's just say it's just a device.
Your first stop is to detect if it's wirelessly capable or not. If it's networked, it might just be controlled or commanded remotely as a lone device. If it's not wireless, then it's operating on a set of instructions given to it before you got there. In case A, you can start hacking the thing no problem. In case B, you have the problem of needing to get close enough to it to plug in a physical cable. So, in case A, just start hacking. You would have to worry about Noise and such, but it's a normal hack into a device you can see on the wireless. At that point, you getting the FlySpy closer to the Lynx isn't going to help your hacking, unless your commlink has SUPER small range or the Noise is so great, you can't cut through it. But, if you can't, I don't know how well your FlySpy will be able to, unless you also had an RCC and were a decker-rigger.
Now, let's assume case B. Here, you have no way to get the cable there yourself. However, if your FlySpy had it's own USB (I'm just gonna call it that, because that's basically what it is) cable and it could use it to find a port on the Lynx successfully, then I would allow a hack to happen through the FlySpy. The decker would have to get permission to put marks onto the rigger's PAN or on the FlySpy itself so the decker could jump to the FlySpy's node and hack that way. However, still understand that the FlySpy is not an authorized device for the Lynx. It doesn't get marks into the system at all. You still need to hack the Lynx. Though, I would consider that your hack is now a direct connect for the purposes of getting around the OS. Since OS only logs illegal activity while you're wirelessly hacking or hacking into a corporation, you get around all of that by being directly plugged into it. Some could argue that the source of the hack is still happening wirelessly, but I contend that the wireless wouldn't have a way of knowing this unless it could deeply read into what's going on, which it wouldn't be set up to do.
This is a case where you have to use as much logical thought about the context of what you're doing to solve the problem. That's basically what I've done above. Of course, people can contend with me about things, but if I'm the story teller and there's no easy definition for this, I go with my logical thinking of this problem, which is how we come to my answer. Shadowrun sometimes has that happen...you just have to roll with what you have as a Player/GM.