"Cartridge emulators have two advantages: improved high-speed compression damping, and the separation of compression and rebound damping adjustments. Rebound damping is set simply by changing the weight of the fork oil (same damping holes for rebound), then the compression damping is set by adjusting the spring on the shim stack."
This doesn't conform to your recommendation to weld the holes shut"
Well I have also read multiple accounts for welding holes shut too, some of which came from the manufacture of emulators.
I was skeptical as well, which is why I didn't weld my rods at first. . . Instead, I took my forks completely apart three separate times, playing around with 10W, 15W, and 20W, and trying welding just one of the holes shut, before finally welding both of them shut.
I'm not sure why there are different opinions on the topic, probably due to different bikes and inherent geometry?
I couldn't say. I just know what I did, and had to do to my CB750 to get the rebound to fall in line.
"If the holes are gone what effect can oil weight have on rebound dampening?"
Thicker oil still has a more difficult time passing through the forks, around the damper seal, through the emulator,etc thereby affecting both rebound AND compression. If you move to a thicker oil for damping, you have to tune your emulators around that. I am by no means a suspension expert, but with both of my holes welded shut and with 15W oil, the rebound is a lot more well behaved then before (I'm still toying with the idea of trying 20W oil just for kicks to see if that slows it down even more!).
Hope this helps, and keep us posted on YOUR results!