Wow, this thread grew while I was away.
They seem to do that, I've noticed.
Reading some of the "verisimilitude" arguments in this thread, I'm left wondering how many of the same people who say "you can never ever hurt the 'greats' because that's realistic" also say to the PCs "No matter how powerful they get, no one will be truly safe from a random punk with a gun because that's realistic." They can't both be true 
. If no one is safe from a punk with a gun, why can't a punk with a gun kill one of those NPCs given the right circumstances? I tend to find that, in general, these NPCs are a lot more untouchable in the minds of certain players than in the actual text.
I think the difference is one of scale. Getting a punk with a gun in a spot to splatter the brains of the top-of-the-food-chain-NPCs against the wall vs getting them in place to do the same vs the PCs or, say a middle-management NPC is that the TOTFCNPCs didn't get there by accident. They got there through brains, firepower, luck, supernatural advantage in some cases, and hard experience. It should be
tremendously difficult to get the drop on them and if you manage to do so, well, that's why they have those contingency-plan-quickened/anchored/what-have-you ultra-high rating spells and spirits for. Add in the fact that most of the beings that are on the "functionally immortal" list have been around for so long that just by being that old they have seen quite a bit of what people are capable of, so surprising them is just that much more difficult. Anyone can die, but geeking Joe Manager is going to be a
lot easier to accomplish than geeking Damien Knight. So much so that I would think it wouldn't actually be worth the effort to do so, and even if it is (Art Dankwalkther comes to mind) the other mega-entities of the setting will see fit to make you not a threat to their status quo. *shrug* I'd say to my players that if you want a shot at Lofwyr or Ghostwalker, start saving up for the leonization treatments or brainwashing adherents, 'cause you're going to need to play the same long game they do to do so, which tends to be beyond the scope of the game.
Well, that was rather long-winded of me. TL;DR: They're not un-killable, just probably not worth the stupidly huge amount of difficulty to do so.
Which brings us back around to the "retribution" argument. Mirikon basically says "if you don't do anything too bad, the corps won't even notice you, but pissing someone specific off is certain death". But that archetypal run I mentioned does involve doing something "bad enough" - you're stealing vital research! Or maybe extracting a disgruntled genius along with his irreplaceable body of work. Ares would be a lot angrier about that than about someone stealing Knight's gun collection, and yet they somehow can't do anything about it as long as the players are following the script.
For a more concrete example, you have Ghost Cartels, where the PCs get to kill the top Yakuza boss in Seattle and get away with it. And there's a Missions adventure that asks PCs to blow up the Brooklin Bridge and expects them to still be around for the rest of the campaign if they succeed. There's less retribution thrown at the PCs for going through those published adventures than there is for them going off the rails and stealing cars in that Dumpshock thread I mentioned. So my thesis is that this sort of invincible retaliation is more often a punishment for deviating from the script than it is a logical consequence of the setting, which is after all about doing daring heists and living to tell the tale.
This I agree and disagree with you on. There's a certain suspension of disbelief that has to exist for Shadowrun to even exist, vis á vis the realism of the response to a team's actions. So I would expect that if the setting says "losses due to shadowruns are built into the bottom line as a cost of doing business" that corps would only bring down the thunder (or Thor shots as the case may be) on actions that would cripple them (which most teams simply aren't capable of by themselves), rather than simply cause them to lose .01% of that fiscal year's profit margins. Pride, though, becomes a different matter and that's what you're generally hitting if you do something against the mega-powers of the setting. That said, icing the oyabun of Seatle seems a bit far-fetched, at least for a team not composed of "prime runners". So I agree with you there. The Missions stuff I tend to give a bit of a pass to, as it's for conventions and not long-term play, so I guess I expect a certain degree of railroading and "no you can't kill them" if only to keep in the time restrictions of the 'con.
As for the specific thread you mention on Dumpshock...that just seemed silly to me, on both sides. If your players want to do that to the exclusion of what you as the GM are trying to do, maybe it's just time for someone else to run a different game. That way (hopefully) both sides can have fun.
