Tony M:
You are right that the great holes on links courses do not usually come at the very end, and you've got one of the two reasons why.
The other reason is that all those courses were designed for match play, and it makes no sense to save the most compelling hole for last, when the majority of matches will be over by then. Darwin wrote that it was "the duty of every good golf course to have a great 17th hole," because that's where matches are ended or sent to the 18th.