I have beat Pokemon Super Mystery Dungeon, obtained Hoopa, and I use it a lot, but it has never changed to his unbound form in a dungeon. So how does it happen?
The form Hoopa comes in is random whenever you summon it in a dungeon. There aren't any items you can use to make it change forms.
Source: This and this.
I believe it depends on the floor number. Unbound, I believe, is any odd numbered floor, and confined is any even numbered floor.