This isn't the official Nexon forums, this isn't the place to post rampant paranoia.
Most of this crap is from people on the official forums that wouldn't know /dev/null from a hole in the ground.
Those aren't logs, users can
optionally set them up manually to input their secondary (not primary) password into the game for them, it's not transferred anywhere, and "hacking" it would require their computer itself being hacked (to browse the file manually or read the RAM data), which is a federal offense, and would allow the hacker to get at their pass info regardless of if that mod was used or not, etc.
Like there's so much wrong with that assumption that it'd take paragraphs to cover it.
EDIT: Not that I'm saying the shops aren't on stolen accounts, they could very well be, but anything beyond "there's a hacked account selling off goods with a specific shop title" is wild mass guessing and I've seen enough BS rumors about this (with little to no backing) today already.
EDIT2: Here's how a report on something like this should actually be done.
http://forum2.nexon.net/showthread.php?1483276-Hacker-Warrning&p=12161773&viewfull=1#post12161773&nxid=10
http://forum2.nexon.net/showthread.php?1483276-Hacker-Warrning&p=12161896&viewfull=1#post12161896&nxid=10
Statments from Sabina, confirming the issue exists
but not extrapolating on details that aren't actually known. A confirmation of what is known and a proper warning and no more.