My character works for Cedric (rival of Bates). I finished the 'Black mountain clan' quest. When I return to talk with Bates, all his guards turn hostile to me and he just disappeared. Where is he hiding :-?
If you have stolen Bates' journal and given it to Cedric, then Bates goes into hiding from shame and hires assassins to kill you. You'll never see him again.
A more fun alternative is to kill Bates to get the journal. The assassins still come after you, but you can say with a smile on your face that you killed the most powerful man in Arcanum. And you can buy his house. But, rroyo is right; Bates is gone for good (and you can't kill him now). I supposed if you really want to you can cleanse his house of vermin (read; guards), or even kill Cedric for being so jealous. I must be a surpressed sociopath, if all I like in this game is killing in the name of nihilism....
The assassins are random encounters, like the Hand. As for buying the mansion, kill Bates, kill all the guards and staff, then sleep until morning. At the west end of the street the mansion is on there will be a man standing there. Talk to him. If your persuasion is high enough, you can buy the place for as little as 50,000. After you are the owner, the townsfolk act a little more kindly towards you.
Actually, I've cleaned the Mansion and then run up the street to find the estate agent already waiting, saying how he's been trying to sell the place for weeks...