With a simple hand drill and a small drill bit, you can just drill out the stock nut (takes about 2 minutes). It's not some super hardened item. Also, if you do safety wire it, then go ahead and loctite it.
As for the valve retainers, it's a matter of time when someone will break one. I just broke one at Lime Rock and the last time that happened was in 2005. On the other hand, every engine rebuild I do, the car gets brand new retainers, springs and valves (the old ones go right in the garbage). I guess fate caught up with me. I know other teams that had plenty of failures but they were just reusing the old retainers. Since we have to run the stock stuff, I just change out the parts more often. Since the retainers are dirt cheap, it's cheap insurance (same for the springs and valves).
When we ran the Z3's with the 2.8l motor, we used to rev them to 7500. They broke retainers all of the time and GA let us run an aftermarket one. Then the problem was solved. With the 330, they put the kabosh on that.
My suggestion would be to change out the seals, valves, springs and retainers when you decide to pull the head for a rebuild. Also, the new valves are ready to use, no machining necessary.