Percentage wise are we sure it's actually that many? Although the exact number of accounts seems to vary depending on where you read it, Naoki Yoshida wrote here that they've experienced 325,000 simultaneous connections so it doesn't seem unreasonable to believe there are over a million active FFXIV accounts and probably a lot more.
I'm sure that not everyone who has had their account stolen has posted on the forums, but I've seen < 50 people write about having had their account stolen. Even if that was 1/10th of the actual numbers that'd be 500 out of 1,000,000 which is 0.0005% and it's probably an even lower percentage because there's likely more than a million accounts.
If there was a problem SE side, there would be a lot more compromised accounts, so logically, it can only be down to people themselves either using the same usernames and/or passwords on other sites or weak passwords or just security with their computers.
