If you want to Spoof a command to a drone, you have to have performed a Matrix Perception test on the persona, which means catching them logged into the same node you're in, or hacking into their commlink and doing it there. If the perception test was done previously, the rigger might have changed his ID since you did it, requiring a new test.

1.
Before every run, Spoof your ID and have an agent update your drones for access.

2.
Have all your drones run in hidden mode. That way anyone trying to hack them has to use a has to first scan for them (knowing they are there still requires 4 sucesses to find it (p225 SR4). If they don't know how many you have, its suggested it the threshold be 15+ to find the others. After finding the drone's node, they then have to intercept traffic coming from your commlink to it to be able to decrypt it (requiring Sniffer).

Most drones are going to be able to be hacked more easily than the rigger's commlink, so it's likely to be the target of a hack.

3.
Basic defense is the Firewall, get a 5 at chargen and up it to 6 as soon as possible. Encrypt the traffic in and out of the drone. (also mentioned a lot in the last thread).
Don't just leave it though, spend an action or two to alter the encryption, which would reset the test for anyone trying to break it, and should stop hacking attempts that have yet to penetrate the firewall (since you've in effect just changed the "language" the node is speaking)

4.
If you can avoid detection and don't mind the illegal hardware, use Jamming and ECCM to blank out pretty much everyone except yourself and other riggers, who likely have ECCM (will leaving your teams chosen frequencies open for commlink operation) or spot jamming to stop the person hacking, if you know who they are.

So if you look at it, to even get in to your drone, someone has to find it (Sniffer or Scan then Sniffer), decrypt the traffic (Encryption X 2), and hack on the fly (Firewall to Firewall +6). If you have a truly uber hacker, possibly spending edge, it still takes 3-4 IP minimum to hack in if you take the basic precautions. If you have a 12 dice pool for each test, roughly 11 IP before they can hack into a drone on average(4 hits for scan, 3 for sniffer, 12 for decrypting, and 12 for hacking on the fly).

5.
Add an Agent loaded with programs from your commlink but running independently on the drone (takes 1 spot in your subscription list and 1 program spot on the drone) with Analyze, Stealth, Attack, and Track with instructions to monitor the drone (track any persona/subscription to the drone and if it isn't from you, begin attacking, or something along those lines). You could even break it into 2 Agents, one to attack, one to track, both with stealth. Each Agent counts against your subscription limit so you can't do this for that many drones. Assuming your GM is willing to make some house rules (depending on your interpretation of IC) these can be installed on the drone itself, and then only the drone takes up a subscription spot. But then would likely have to depend on an alert or hacker glitch to trigger the IC instead of having an Agent always analyzing for intruders.
The fluff talks about even cyberarms having basic defensive programs to protect against hacking, so there is at least some basis for this.

6. Having a physical emergency shutdown switch or LOS laser receiver for ranged shutdown if you do lose control is also a possible option, but if the enemy knows about it, you will loose all your little friends.

Now, a person that makes a living stealing drones is going to prepare for it, and be good at it if he going to survive. They will use Agents to Scan and Sniff at the same time, Agent's to hack multiple drones in unison, spot jammers to interfere with your connection or the drone to keep it from recieving new instructions, and a whole lot of other things I'm just not thinking of right now.