There was an article published in the July/August 1975 issue of The American Blade, also by William R. Williamson. In the article he speculates that the notches could have been for nail pulling, religious purposes, cutting sinew when skinning, or for blade catching. He concludes that notches were originnally for cutting cord or twine, which would explain their positioning on the blade (most were behind the choil, precluding the use of the notch as a blade catcher). Undoubtedly the notches were used for other purposes as the use of that type of blade widened, and different cultures were exposed to it.
Percussion caps did not come into existence until after the notches had already been on knives (they seem to begin somewhere in the mid to late 18th century).
Of all of the explanations that i've heard, William's sounds the most plausible. The knives were used by sailors, and Williams speculates that the notched-knives were used for working on nets, sails, etc. As other people came into contact with the notched-knives, they probably used them for some of the other uses mentioned.
Regards,
David