I was hacked, and I'm an honest player. I don't visit gold seller sites, use their services, or even associate with players who have if I'm aware of their activities. The only things that I use that aren't directly related to the client are addons that I get through curse.
If you've been keylogged, chances are they're gonna get your secondary password anyway (presuming the intent of the keylogger is to get at your characters assets and not some other asset), having to use your secondary password to log in as well only makes that task easier, it wasn't impossible before.
Like others have noted, the frequency of this happening is every single logon - I rarely ever bought or used diamonds....a login 8 times a day (okay, more with crashes) vs. a login once every 3 months is less secure for me by far.
The bigger problem, regardless of actually being hacked, is this: I have not heard a lot of positive accounts of people getting their characters/accounts back after being hacked. If it was as easy as them going "oh, look, your IP was this, and obviously someone hacked you from a different IP, took all your stuff...here, let's get you your things back...." like some other game I know, then I would not be paranoid. I don't think that is how it works on this game. I *may* be wrong. But it seems that a F2P game where people spend money should have a recovery team for when things like this happen, instead of having to start all over again - after all, how many people spend hundreds a year on Runes, not even thinking about it....
If I could ultimately feel safe knowing that if my account was ever stolen, I would have people working on recovering it (hell, even for a fee!!!), I would rest a lot easier.
There are other various programs out there to tell you who and how people are accessing your system outside of the game. Do some research and learn but I warn it is a medium grade of a learning curve but well worth it if you really want to be protected.
Again, if you have *anyone* sharing your system (kids, wife, husband)...all it takes is 2 seconds of them clicking an allow alert, or installing something when you're not there. Not all of us can afford to have computers for everyone, and ultimately, the weakness of the best AV out there lies with the user and what they allow as far as program alerts asking for permission.
I just wish there was an easier way to reset the thing. It's insane that I have to submit a support ticket to have it reset, just because I haven't been able to play in a while and can't remember it. Don't the CS people have more important tickets to deal with?

^ this....we need to have this password be able to reset securely - why not through email verification with the email registered to the account? This works for most other games I've played. They'd have to hijack your email accounts too to get your account.