I've spent a little time on this myself, so I thought I'd chime in here.
First off, go here:
http://www.shadowrun4.com/resources/faq.shtml#6 (second question). That's pretty much how you do it. They have device ratings. If they're using Alphaware or above I'd raise either the device rating by one per upgrade (+1 A, +2 B, +3 D) or add other protective measures (like IC or similar).
That's how you run it. Fudge what you need to IMO because when it happens it should be good fun and give Karma.
Now, to all the naysayers talking about the inability to hack cyber because of no wireless connections, ect... I'll quote from that FAQ here, "Most cyberware has a direct neural interface, allowing the character to mentally access and control the implant,
[b]but wireless links are also included in case the character is unconscious or suffering from extreme trauma -- that way medtechs can easily detect implants and check them out. For example, you'd certainly want a medtech to know you have an internal air tank before they take a bone saw to your ribcage, so expect that implant to have a wireless link.[/b]"
That means that EVERY cyber that would have a wireless link (aka everything other than dermal plating or whatever) HAS a wireless link. End of story. YES, you CAN turn it off, but doing so requires a few special things:
1) The skills to do it yourself without frying your central nervous system when you mod your own MbW.
2) A REALLY good friend with the skills to do it without killing you in the process and who you TRUST can do it without killing you in the process.
3) A talented team mate who's willing to do it for you who you can trust not to either
A) Fry your central nervous system
B) Leave a backdoor for themselves to easily ice your ass when you betray them/they betray you
C) Sell the access codes to your internal Air Tank to an opposing SR team so they can blow your ass up like a balloon
4) If you've got a talented team mate who you can trust and who can do the job, there's that silly COST to worry about (few runners will sell their services to a Johnson but then give them away to team mates just cause).
5) Enough dough to hire a talented Hacker/TM who can do it for you, and the connections to find one who's trustworthy.
6) The flat out CASH to have customized ware built for you when you get your shiny new implants and have them set the way you want them for security when you buy them. Meaning
A) They're now probably Delta grade ware.
B) They cost a TON more thanks to specific modifications and optimizations you want installed.
C) When you get shot in the back during a run and your MbW III Delta Customized ware is damage, you're going to shell out 10x more than you normally would to get it fixed, oh, and you're harder to treat thanks to your insane level of paranoia having the MEDICAL INTERFACE TURNED OFF
Now, that being said, YES, you can go and have your gear secured by not having a wireless connection. You've spent yourself a TON more cash to do it, but, HEY, you're secure, right?
Now, the SMART runner would simply have the hacker they're working with maintain security on your groups PAN (you're running TacSoft anyway, so he SHOULD be doing that already). Have him load some optimized IC on each of your commlinks (only need one copy of the IC, and copy it to everyone) and put a few Data Bombs in the access areas for your cyber-signals and you're done.
See, shutting OFF the cyber's wireless signal is both expensive and dangerous. Having your team's hacker PROTECT the team's cyber is FREE and SAFE.
Also, when it comes to NPCs, please, please, PLEASE, keep the above list in mind. A group of Go-Gangers or Lone Star or even a spec ops team isn't going to spend a BAJILLION NuYen securing EVERY piece of cyber in them. They don't have that kind of resources unless it's company supplied. And even then the company's not going to supply it due to cost considerations unless you're sending your group against Ares or Aztechnology. And if you are sending them there, hacking a response team's cyber isn't going to help much in the long run.
The rules for hacking cyber are there for a pretty good reason IMO. It CAN be done. And it gives the non drone hacker/TM something to do in a firefight other than shoot once and duck for cover. The Sammies will go 3x per round shooting 2x or more per IP anyway. Let the Hacker try to shut off Goon #1's Wired Reflexes. The Sammie can kill them in 1-2 rounds, the hacker can shut them down in the same amount of time really (figure 1 or 2 IPs to find the signal for their com, 1-2 to hack the com, 1 for sending the spoof and another for the reboot to take effect which boils down to 1-2 rounds as well) If you let the hacker shut off a Cybered goon, then you've got a team member who is effectively eliminating a threat without killing them. And most SR encounters happen because the team failed to avoid having to kill them anyhow. Wouldn't it be nice if you had a guy on the team who could shut down some of the enemies without having to kill them?