I guess I'm not quite sure what the question is as far as how Anarchy holds up as a gaming system. Are we talking about long-term progression and whether things eventually break down?
I've been running an Anarchy campaign for about two years now, although there have been periods of inactivity so we're still in the "dozens of karma" range rather than "hundreds of karma".
My personal experience is that long-term progression is one of Anarchy's strengths. I think the Amp system is inherently much more balanced than the regular Shadowrun rules. I did implement one house rule so that Essence wouldn't constrain mundanes unduly:
"An individual piece of bioware and cyberware will never cost more than its base Essence, even if you upgrade it. Cyberarms will never cost more than 1 Essence, for example, no matter what their shadow amp level is. This is to provide mundane characters an equal opportunity to advance as Awakened characters without being limited by Essence."
Other than that, I like Anarchy's karma costs. I feel like they are balanced and provide an equal incentive to improve skills, attributes, equipment, and shadow amps in equal measure. My players, for example, did not just pour all of their karma into Amps, which I took to be a good thing since that was one of my concerns when the game started.
I can't tell you if things break down at the 100+ karma level, but right now it doesn't appear to be a concern.