Here is how I currently do things.
It never occurred to me to use any thread but silk when I do work with pearls for myself and customers...other than pearls mixed with stones/metals that might tear or fray the silk (gemstone beads from India, in particular, are highly irregular and sometimes jagged inside). I use silk because, when I learned all this, I was told people expect silk under pearls. I have no good reason other than its the way I was taught and the way I always do it. I am open to trying nylon as I can't stand stretched out silk, but I wouldn't feel comfortable selling a piece done in nylon at this time because of the expectation that knotting is to be done on silk. Narrow-minded....yes.
I also believe there is something to be said for the proper preparation of the silk. I manually stretch mine twice. Then I run it through a cake of beeswax and then stretch it again. I also pull on it strongly as I knot. Ideally, this helps to prevent stretching out in the near future.
I also understand what someone said a while back about the feel of silk. Sure, you can't tell when you are wearing it. But, while you work with it, it feels nicer flowing through your fingers. More specifically, I absolutely love the feel of Gudebrod moving over my fingers. It's much softer than Griffin. Gudebrod seems to stretch out more, though and no needle! Griffin's disadvantage is that the knots look bulkier...especially the beginning and ending knots...bleck. It almost makes me wonder why many professionals insist that french wire is the only way to go. Precious metal end caps, to me look far more finished.
At my local jewelry store I recently saw a very expensive akoya necklace finished with open bead tips (not clamshell) and an ugly knot spilling out over it. Not that mine would look much better with that kind of ending. But I just wonder about the industry standards and if they are always right...kind of like Caitlyn was saying about "why silk."
Heavens...that's a lot to say about thread!!