Don't take this personal if I'm wrong, but it looks like in whatever runner bar you happen to end up in, you can't spit without hitting a violent psychopath armed to the teeth with highly lethal weapons. Yeah, I get it. The world is a big sack of crap, neither the corps nor the govs give the proverbial flying one about you, and the only way you can survive is if you pack enough heat to turn a Kamikaze'd rhino into red mist. But sometimes I look at people I work with, and I can't help but think that a prerequisite to becoming a runner is having one's empathy surgically removed.
Anyways. *gets off high horse*
Morality aside, there are obvious advantages to the non-lethal approach. One, you're not wanted for murder, only assault. Two, the friends, family, and employers of that security guard you knocked out are less likely to come gunning for you (or send your colleagues to do the job for them) than those of the one you turned into wallpaper. Three, non-lethal agents come in a variety of nifty, fast-acting, SILENT packages, which your average opposition tends not to protect themselves against.
Thoughts, preferences, tactics?
Well, this is where it falls on the GM to set the tone, not just for the current game, but for each neighborhood. You visit a Runner watering hole in the barrens, expect to need at least a heavy pistol, if not not a machine pistol to set the tone of "don't frag with me" to the other patrons. (and they may still frag with you if you act like an ass)
However, in the glittzy downtown core of Seattle where the well to do go to blow off steam, even a light pistol could prevent your entrance to a club. These people pay well for their protection (to KE) and expect to be protected from gun toting drunken maniacs (IE: everyone but them). And they expect the clubs to help keep them safe, which means preventing armed individuals from going in. ("yes sir, I see your pistol permit on your SIN, but we have a strict no weapons policy. Leave the gun in your car, or you're not getting in")
As for the lethality of runners, again this is up to the GM to 'enforce'. If the players leave a mass of butchered bodies behind them after a run, the media attention should be through the roof! ("Is there a gang war brewing in your neighborhood!? Over twenty men, women and children where violently butchered on the streets of Seattle today! Find out where on channel 7, news at 11") Even assaults with high counts will be investigated (but MUCH less man hours).
Keep in mind too that Corps are always concerned with the bottom line and productivity. A bunch of beat up security personelle is alot cheaper then alot of dead security personelle, not to mention easier to hide from the corporate wage slave masses. (after all a bunch of scared wage slaves are not as productive as happy wage slaves). Then there is "Corp Pride/honor/responsibility" to consider. 20 battered security guards might net you full co-operation of the corp with KE/LS and a dozen hours or so of the corp's elite sniffers looking for you. 20 DEAD guards would probably net you 200-300 man hours of sniffers hunting you PLUS a Black Ops strike. They have to send the message that killing their citizens is NOT tolerated!
Then their is the Johnson AND Fixer to consider. Yes, some Johnsons want or even expect a high body count (depending on the run) but usually they want things as quiet as possible to avoid notice themselves. After all the SOLE reason to use a SR team is deniability, that way the sponsor Corp isn't liable for the damages/thieft. And let's face it, if a Corp wants a bloodbath that could be tracked back to them, they'd just use their own special forces teams (FireWatch, Red Samurai, etc). The Fixer who set up the team has his own rep to consider as well. If he gets known for giving jobs to blood soaked maniacs, he's going to lose the custom of everyone who wants things done 'low-key', not to mention the heat he's going to attract from authorities (Corps, gov't, police of all branches). A fixer who has 'the man' following him everywhere he goes can't really do his job as a fixer can he?
In short, less-than-lethal should be a Runners credo 99% of the time. With that lethal option for only when it truly; A) doesn't matter (deep in a Z zone) or B) no other way to escape. If the lethal option is a Runners first (or only) choice in every situation, expect to have a short, bloody, pain filled career!
Unless, of course the lethal game is the one your GM wants to run! Then break out the full autos and goto town!