I haven't read Bud's article, so I don't know if the OP misinterpreted something that he said, but the bottom line is "what is standard aircraft practice"?
Just because someone well respected writes a mag. article that deviates from long standing and well documented (AC 43.13, Aircraft Standards books, etc.), does that mean everyone should should suddenly change?
It is a long term industry standard (practice) that cotter pin safetied nuts be used on any fastener that is exposed to any level of rotation (a fastener where something that can move is actually pivoting on the fastener).
In almost every example I can think of on RV's where something moves, the rotating part/assembly is pivoting on a bushing or bearing that is captured by the bolt installed with the AN365 nut (the bolt is torqued to normal value and can not be rotated). In the few instances where a bolt is used as a pivot point (fwd and aft ends of rudder cables is a good example), a castle nut and cotter pin is specified.
Tangent - In fact, I would argue that in some instances, a cotterpin safetied nut could be more dangerous than a nylock one. Keep in mind, these airplanes are for the most part built by amateurs, so it is amateur level skills that are installing the cotter pins. How hard can it be you say? It is not. But there are different techniques that can be used to make them safer.
Lets say for example you have cotter pinned bolts on the aileron hing points. They are somewhat low to the ground (particularly the inboard one). Now lets say you are at a remote grass strip and while taxiing you swing you wing through some very tall grass that catches on the legs of the cotter pin (that was installed by an amateur) and bends them open, and at some time later the cotter pin falls out. Given that there is a chance of it occuring, which kind of nut would you rather have installed, if an AN365 is "by standard practice" totally exceptable?
Now I realize that the cotter pin has two legs and they should be bent in different directions, etc., etc., but this is a real scenario. I am aware of cotter pins being lost from rudder cables on tail draggers that regularly get run through tall grass, or on rudder pedals from peoples shoes, because the bolt wasn't oriented to prevent shoe contact.
My main point is "do not become complacent and assume that just because an AN365 nut has been replaced and is now safetied with a cotter pin, that it is automatically safer".