Is it safe to drill my rim to accommodate a larger nipple size?

I think the stock nipples are 6mm and I have a set of 8mm.

 

You need to check to make sure the spoke is not also larger. I don't see much benefit from the larger nipple alone, except a slight bit more flat when tightening.

If you drill you need to try to make sure you are drilling in the direction the original hole is aligned.

I know somewhere along the line Kaw had heavier gauge spokes, don't remember if it was early or late models.

 

I'm going to try drilling on my bad rim first.
If that goes ok, I'll drill the good rim and then I can get to lacing the wheel.
Riding season is here and my bike is on the jack.

 

On my 2014 klx250s the spokes are 4 mm pretty heavy duty, the older ones were 3mm