Ipv6 would run as a dual stack so unless your retarded and set AAA records or ipv6 access there will be ZERO PROBLEMS if you do you suffer from a layer 8 problem

The problem with encrypted p2p is that you have to trust the other peers/trackers because if the RIAA gets into your p2p network they can see what your sharing or just get a nice list of peers for a torrent. All your doing is evading packet sniffing and increasing overhead on the program.