Just because it changes doesn’t mean it‘s bad.
Even your only point where one could argue that there is a potential obvious negative health effect (the vitamins) is only an issue if there are actual vitamin deficiencies that matter.
It's an issue because it's wasteful, you're loosing the good stuff in the process. Throwing half of your meal into garbage every time is only an issue if you're still hungry afterwards, but it's not economically and ecologically sane thing to do. This is a similar thing, one should try to maximize the use of food that they pay for.
You waste much more by not cooking them.
On the other hand some processing like canning of fresh food can actually help preserve the good stuff compared to whole food that's refrigerated or otherwise stored over longer periods of time. Processing also can increase the bio-availability of many ingredients, which can sometimes be a good thing, or in case of sugars not so good.
Processing changes so many things in both good and bad ways that you can't use its presence to determine much of anything.
Have you ever for example looked at how many vitamins are destroyed 50%+ just be heating food and even minerals become less absorbable.
All the enzymes get killed by heating over merely over 45deg C.
The fats also change during heating.
The proteins change during heating.
Then there is the Maliard reaction which is a reaction of carbohydrates + protein which creates a totaly new byproduct (this is eg why bread browns).