It's because hisoka fought chrollo and chrollo used the phantom troupes powers to aid him in the fight, so he's going to kill them all in order to have a fair fight with chrollo.
because killing the user removes the ability from chrollo's book.
I think Gon will end up tracking down and joining the Phantom Troupe in order to regain the ability to use nen again. Also his nen category will probably change in the process. He may end up becoming a Conjurer or a Specialist.