What's the difference how a phone is unlocked?

I'm prompted to ask this as I just won a bid on an unlocked 3GS on eBay. Someone pointed out, and I quote, "90%+ of the "unlocked" iPhones sold on eBay are hacked to unlock them or jailbroken, NOT legitimately unlocked."

Can someone explains how this may effect the phone's performance or anything else?

Thanks.