Well, I knew it was only a matter of time before the RMT account thieves started targeting XIV...
Best bet is to contact SE customer service via email or online chat. http://support.na.square-enix.com/faqtop.php?id=902&la=1&c=3&SQEXSC=afd448sdj6f29atadtmdp2h1u4#FAQ
Also, buy a security token if you ever plan on playing any popular MMORPG, if the company offers one. http://support.na.square-enix.com/faqtop.php?id=902&la=1&c=4#FAQ
Finally, never use your login info online, except on the official Lodestone pages and SE account pages. Never use the same info you use for your SE account (Pw/username) for any other accounts, as well. http://lodestone.finalfantasyxiv.com/pl/index.html https://secure.square-enix.com/account/app/svc/login?cont=account
In answer to your questions.
1. Yes. It is quite common in other popular MMORPGS.
2. SE can choose to reverse the trades or roll back your character as they see fit. It's not very hard for an experienced GM to find where the items went and at what time.
3. Unless you know where the account thief lives, they will not be punished. Generally speaking, RMT groups, which account thefts are directly linked to, operate in areas in which Japanese and American law cannot touch them. If you know who the actual thief is, I suggest dispensing justice yourself, as it is the only way you will have it occur due to the lack of laws regarding this issue.
Now here's some things you're going to need to do, now that you know your computer has been compromised.
1. Change all your account passwords on another computer. Also make a new email and link the accounts to it.
2. Wipe it completely. Your computer is not safe, and you may even want to buy a new Hard Drive and reinstall your OS on it.
3. Check your bank records for unauthorized transactions. If the thief got a hold of your personal info, sometimes these transactions can be traced by the bank to find the thief.
4. Once your computer has been made safe, install proper anti-virus software. An ounce of prevention is worth a pound of cure.
5. Last thing you need to do is chill out and have some fun, once you made sure your computer is safe and your money hasn't been touched by whoever got a trojan on your computer. Go out, eat some good food, maybe play at an arcade or see a movie. Just relax.
Edited for various grammatical errors. Edited, Jan 18th 2011 6:50am by Uryuu