I just lapped my Ninja last week because it was concave and had a nice little divot near the center. Just sat down with varying grades of sandpaper up to 2000 grit, zoned out to the idiot box for a few hours, and didn't stop until it was as flat as possible. Then for kicks, I did the same to my 165, although I stopped just shy of lapping the serial number and stepping code to unreadability in case I ever want to sell this one.
What was the result?
Well, after four hours of lapping, reinstalling the CPU and HS resulted in an immediate 5c drop in temps, and this was comparing a fresh bead of AS5 to the old coating that had set in.
In my opinion, flatness is the only important thing to worry about. While grinding the surface down to a mirror finish is nice, flatness is far more important. I lapped the base of the Ninja and the IHS on my 165 until I started to get a nice hermetic seal, and it certainly paid off; where my load temps were 46c before lapping, they don't pass 39c at the same speed and voltage.