When BB, Target, or CC clearances a game, it means they will no longer be stocking it.
Essentially, it sat on the shelves too long and they want to make room for the next "hit" title. If u look around, there are plenty of copies about, but I imagine, like the first one, it will be increasingly harder to find.
BTW - FF2 was just announced for XBox today, complete with a new first person mode. More Tecmo love for MS.