I guess it is probably a case by case basis answer...there are so many variables for each example that you can't really generalize.
Trees are planted, and they grow too big, are hit by lightning, etc., so some change is good (perhaps removing a tree that grew too big or was planted in the wrong place when not accounting for growth), and some change are inevitable (trees get hit by lightning and succumb to wind) so that change is natural and perhaps irreversable.
Bunkers can evolve, as I am sure that most of the bunkers on the Old Course might not have been there at all or in their present form 200, 300 or more years ago on the 'original' design. Sheep, the wind, divots, orwhatever created those bunkers over time, as I am sure did some rework by architects or greenkeepers here and there, whether intentional or incidental.
Other bunkers on courses need to be redone due to inadequate maintenance over the years, or weather changes that made a bunker less penal (or maybe more/too penal) than designed.
I would say you have to look at each bunker, tree, etc. and decide 1) whether the hazard is in line with the architect's original design and desires, 2)whether those desires were legitimate or apply to today's game, and 3) whether weather (try saying that quickly) or other extremes have caused the change in the hazard, and whether this has been a positive or negative change for the hole and course's health and playability.