At least one is pretty much guaranteed to escape again and start a new dalek army somewhere. Or somebody will open another prison somewhere. Or something.
Thing is though, even if the time war gathered all the time lords and daleks together from wherever they were in history and killed them, it should still be possible to encounter them in other time periods at times which in thier personal timelines are prior to the war.
Time to turn on my fanyliser. You can't access them in their personal timeline because the timewar actually damaged the universal timeline, erasing daleks and time lords from all history (as army of ghosts showed, this only occured within the universe).
My theory is that when the face of bo said you are not alone he was talking about the Master. However he was not referring to the fact that he was another time lord but to the fact that he is actually the doctors brother. This idea was originally planned years ago when the master was played by a actor called Roger Delgado however the actor was killed in a car accident before they could write a script or film it and the idea was abandoned. I think RTD will go with this idea as it would be a huge shock and totally unexpected for him to screw with doctor who history. Thatís just my theory though I could be totally wrong.
If the master is Saxon, as played by John Simms, that would be brill. He's a great actor, right amount of creepy charm. However I always thought the master was a bit bollocks. The only good stories are where his motives are survival and revenge, like in The Deadly Assassin and Survival. Otherwise he's just another camp, OTT doctor who villain.