All the megacorporations, to one degree or another, must necessarily accept a certain degree of lost revenue, scuttled projects, and poached assets as just the cost of doing business. After all, for every shadowrun against your company, you’ve probably ordered one against a rival.
The trick is to play the long game. Mr. Johnson can lose a few million nuyen in Q1 as long as he can make it up in Q2... Keep your department in the black and maintain a figleaf of plausible deniability over your use of “special assets,” and he’ll be okay.
Lowfyr, on the other hand, is playing the very long game. A dragon doesn’t worry about quarterly profits and fiscal years, and a great dragon doesn’t really worry about money. Lowfyr’s using S-K as a means to an end, not an end in itself.
This is the key. There is a certain level of pain you are willing to accept as the price of doing business. You can try to mitigate it somewhat, but the only methods for eliminating it are too (pardon the term) draconian to work in the long term, especially for a corporation the size of S-K.
As with most corps, you'll have 'low-hanging fruit' in certain divisions, and picking some of those fruits is fine. You get caught doing it, or you get greedy and start picking so many that it becomes a problem, then you're going to have troubles. The closer you get to upper management or Lofwyr's pet projects, the lower the pain tolerance is going to be, the tighter the security, and so on.
Making a run on an S-K factory to sabotage the first run of some new electronics? That's not going to get you a dragon's personal attention. Hitting the factory's financials so that you siphoned off a few hundred thousand nuyen? That's going to have someone paid to find you. Running directly at the head of S-K North America? You're going to be in deep drek if there are any ties back to you.
However, Lofwyr is also practical. Shadowrunners are tools. Breaking the tool that hurt you may be satisfying, but it is better to get the hand that held the tool. Runners who are professional, and do a 'just business' approach, take on all or most of the megas as the jobs come, and so on aren't likely to get high on the hit list unless they run against a high priority target, or leave a bunch of bodies behind on the next run, or something like that. It is the ones that have an axe to grind that will find themselves in hot water, since they often do things to make themselves bigger targets.