The holocron isn't him. A holocron is imprinted with the thoughts and words of the person, but it's not truly him. The only holocron that held a Sith Lord was Darth Andeddu, who hid in his holocron. That's why he was able to use his powers on Krayt from the holocron.
It's been speculated that Darth Nihilus survived. It's unknown whether this line refers to something that occurred before or after the game: "Darth Nihilus - You escaped death by containing your consciousness within your armor. How?"
That could mean that he survived KOTOR II. I personally doubt it, but it's speculation among fans.