You might ask: Does it matter what type of pond, or is because of mainly water quality.
Yes....Water quality is the main factor.You may not like this answer but, it has to do with water quality of course the higher quality the better odds. Aeromonas bacteria counts will be lower and thus allows the Koi immune system to have a better chance to fight it off. If Koi is in a stressed environment the lower the immune status and if bacteria count is high then the odds are koi will get dosed.
Things like debris/mulm/fish poop and whatever nature can throw in pond has an effect. This is one reason why we try to keep the main pond as free of these items as possible, this is done with bottom drains/tpr's/skimmers/aeration and ends up in the settling chamber to be dumped out. If there is a high load of debris/mulm/fish poop this does nothing but to provide a breeding ground for bacteria to establish and grow in count. Lets don't forget overstocking.
This accounts for the debate on rocks in pond, thus slowing down the removal and or trapping in the cracks thus decomposing. Thus allowing bacteria a food source to grow strong and multiply to higher counts.
Now from the other side of the coin; even in a non-rock condition these same factors come into play if the pond was not properly designed and you have dead areas for debris ect to build up. Or under filtered, no pre-filtration. Not enough drains/no skimmers or poorly placed/no aeration or not enough. Over feeding not doing water changes, overstocking which by the way applies for both types of ponds.
Let's don't forget the overfeeding and under filtration, levels of ammonia/nitrite will develop when there is to much food or debris/mulm/fish poop that is breaking down, thus using o2 which then can stress koi when low levels of o2 exist.
This is why it is important to do water changes cleaning of pre-filters/vortex settling chambers/back-flushing.
Bottom line is the cleaner the system it will allow higher water quality, thus keeping bacteria levels low and Koi can then defend against them via natural immune system they have.