I'm sorry, did you miss Harley's always-present defenses that I posted? And that's nothing compared to the Dragons.
I chalk those up to "authorial protection", where "author" here can just as easily mean "the GM of that campaign". I might have missed you quoting the source of those numbers, but to me it seems they were written by starting from the conclusion that "Harlequin is invincible" and working backwards to a set of numbers that seemed sufficiently high to justify that.
A more general answer to the "they have defenses" argument: I get it that these NPCs are powerful. I get that they'll have lots of security in place to protect their sorry hides. Bodyguards, fortresses, magic, and so on. In my opinion, it's okay to state that, and it's okay to design a hellishly hard security scheme around them, should the PCs go after these people for one reason or another. But if the PCs happen to get past all of that through their own creativity and personal power, then it's not okay to make new "unbeatable" defenses on the spot just to force failure upon them. That crosses the line into authorial protection and railroading. If someone is crazy and resourceful enough to stick a high-explosive rocket down a dragon's throat, then it goes down.
And as for the whole retribution thing, the reason 'runners don't usually get too much retribution for their actions is the same reason they aren't a threat to the guys on top: runners are pawns.
Revenge isn't profitable. Hunting down a runner team costs time and money and will be a pain in the ass unless they were stupid and left a bunch of clues
The team in Ghost Cartels framed the Mafia for the hit (...)
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.
I'm answering to all of the above in aggregate as well. I agree that there's a degree of suspension of disbelief involved here. However, I argue that it should be applied
consistently. The rationalizations for why shadowrunners get away with scripted runs where someone hires them apply just as well to runs they perform out of their own personal initiative. Yet the same target is often said to be able and willing to find them and exact revenge when in the later case, but not in the former.
Shadowrunners are called "deniable assets" in corp-speak for a reason. An employer will almost never be willing to take the fall for a runner team they hired, and they'll almost never even help them hide. If the employer is a "power" themselves, the "almost never" becomes "never". If a competent runner team is able to hide from retribution when hired by someone, they should be equally good at it when working for themselves. Cross the mob/corps/dragons and they'll hunt you, sure, but they won't be any more able to
find you than they were the last 50 times you crossed one of them on behalf of some power or other.
Let's take the Ghost Cartels example again, where a top Yakuza boss is assassinated. The runners avoid retribution from that because they frame someone else for the murder. Okay, that's valid. Now let's say that, instead of being hired by someone to do this, they decide to kill the gangster because one of the PCs had their family killed by him years ago. The rest of the group goes along because they got his back. No one hires them to do this. They make a sound plan, get the boss when he's vulnerable, pin the deed on the Mafia, and lay low for a while in another city, just like they'd do in the "for-hire" run. In my mind, they should be just as able to get away with their personal vendetta as they would with a normal run.