Matt,
I won't speak for any classic courses, but I have always worked under the theory that if it is difficult to maintain, or slows up play, or is deemed "unfair" by the right (or wrong) person, it will be changed sooner or later. Given the economy, things are getting changed sooner!
I recently found out from an occaisional poster here that one of my mid level public courses will have some modifications. On one hole, I created a driveable par 4, with an alternate fairway over a large waste bunker. That bunker probably loses a ton of sand a year to wind, and since its on the slice side, it seems it slows play. Lastly, as the budgets are cut, it takes too long too rake. I made the "triple dipper of mistakes, I guess! So, they are changing it to meet their very "here and now" needs. They are not consulting me. Am I upset? Of course not. I understand their needs. I did suggest a way that bunker could be reduced and maintain the same strategy, which I hope they implement.
So, while the course I am discussing is certainly not a classic, it does illustrate that the forces that have caused renovations still continue, and those forces are mostly economic.
Designs continually evolve before and after grassing. I'm sure the architect went through several iterations of both the routing, and once settled, the feature design, before settling on the "final". In fact, the final was probably an evolution itself, with last minute bunker changes, green contour floating etc. You have to grass it some time!
So, who says the first design is the right one? Just as you evaluate a course after playing it a few times, so does the architect and owner. Sometimes, problems come out only then. We all try to balance the design for the "design triange of strategy-maintenance-aesthetics. Sometimes, you only know the maintenance and strategy ends after a few years of experience.
Then, as the story above illustrates, who says there is one right answer for all time? Things happen. Longer shots, new maintenance practices, changing clientele, these all happen. In another thread, we discussed Cedar Crest in Dallas, going from ultra private, to public, to low end public, and perhaps, back to upper end public, during its 70 year lifespan. it also needs to distribute effluent water for the city of Dallas in an acceptable way, something Tillie couldn't know, but is now necessary.
So, maybe, the architect was the one who made the "ill considered decision" in the original design, by not properly considering all sides of the design triangle. Or maybe, things beyond his control happen, or things happen over time, and the course must evlove and change to fit the here and now.
Of course, I'm sure every case is different.