I thought Apple get a hardware list when you send a bug report or update your software through the updater app?
I wouldn't be surprised if system information wasn't sent to Apple more often, but those are the only two that I know of off the top of my head.
You really think software update sends enough info to apple (about every user) for them to not only know you are running a hacked version, but enough personal info for them to take legal action against you?
And even if that was the case, users of hacked versions would just need to avoid sending bug reports and download the updaters instead of using software update.
Except that people have got through on the phone since that article went up, and they've confirmed they haven't been shut down (yet). Just because a website goes down doesn't mean it's because of legal reasons.