I think that the early polyester threads probably had some issues associated with them -- such as being so strong they could saw through cotton fabric. However, polyester threads these days are made with tensile strength very similar to cotton thread, so there really is not a danger anymore of polyester threads sawing through cotton fabric!
I read a blog recently done by someone who repairs vintage quilts. She had a quilt that was made using cotton thread in some seams and polyester thread in other seams. She was having to repair the seams sewn with cotton thread, because it had deteriorated; the seams made with polyester thread did not require repair. However, she noted that the polyester thread had not faded in color as the cotton threads and fabrics had; the polyester was still its original color.
I use polyester thread (Glide) for quilting because it gives me no problems. Plus, I am not making vintage quilts meant to be handed down for generations. I do think that, with machine quilting, polyester thread can be an issue for those making an elaborate quilt meant to be cherished for generations. In other words, for that kind of quilt I would be fine with using polyester thread for quilting, but I might want to use a cotton thread for quilting -- just so all the colors would fade together.
I don't know about silk thread colors. Do they fade like cotton? If I ever were to make a "show" quilt meant to be handed down in the family for generations, and if I were to do machine quilting on it, I would probably want to use a very fine silk thread. I know a lot of the show quilt winners are quilted with silk thread.