One of the guys that taught me uses a grinding spindle (like a large die grinder) mounted in a fixture, spinning a dressed stone about 4" diameter with a hinged plate that he clamps the blade to, and then lifts up to the stone. When properly dressed, he gets quite good results.
I personally prefer using a stone to cut nail nicks as opposed to a fly cutter, and I prefer greatly for my process, being able to cut the nail nicks after grinding, as I heavily taper all my slipjoint blades. It also gives me the ability to adjust spine geometry and keep the nail nicks perfectly parallel or not, depending on what I want, after I've got the geometry dialed in in the closed position.
Everybody has their methods though, I like the dark look of a stamped nail nick and the freedom to get some interesting geometry there also.
Personally, I cut most of my nail nicks on a surface grinder with a larger stone, which is contrary to most things I've read suggested, but I like a very swooped dramatic nail nick, that you can get from certain dressing angles on a larger stone (7"). This is usually the last thing I do before hand finishing the blade, and nailing it all together.