It's funny that SE is only speaking in regards to CT.
It got released early in Hong Kong, as games often do. You didn't see Konami whining about it's latest Castlevania, and sales have been quite good for that.
SE games get pirated to hell. This is a fact. CC, any Final Fantasy, doesn't matter. Chrono Trigger won't be pirated anymore than those games will.
And yet despite that, I still hold that CT will make a lot of money. Why? Because the people they want to buy it, will buy it. And so will the curious consumer.
What they're doing now, is trying to rope in more cash by playing a guilt card on those fans who maybe weren't going to buy it. I don't see them issuing a statement like this with their HUGE releases. Hell, PS2 gets hacked to hell, and they said nothing about XII getting pirated.