Adam:
A couple of the things we've come across in years of looking at old courses:
a) The strategic value of hazards 150-200 yards off the tee on certain lengths of holes, which prompted your thread.
b) Bunkers 50 or more yards apart which overlap visually, and throw off depth perception.
c) Building to a climax at the 16th or 17th hole, because early courses were designed for match play.
d) I'm sure there were a bunch of playing considerations appropos to the stymie rule, which might have been manifested in the architecture, but which nobody today would notice.
It isn't that nobody COULD understand such ideas today, it's that they don't fit with the modern perception of what's fair, so they are dismissed without proper consideration.