They're being built in as much secret as possible because everything is. Everything about land development is adversarial and the people who keep their mouths shut wind up taking fewer 4-7 figure screwings along the way than the honest people.
It sucks that this how it is but even just the most casual familiarity with all the rules and processes makes it obvious why this is the way it is.
You could find more than enough data points to write this same story about grocery stores or anything else.
We, as a society, set up rules to allow the people to have a voice in decisions via various means including public meetings and various review procedures. There is a cost to these rules, but the alternative you're describing is a system where rules and laws don't matter and anyone with the ear of a few influential people can do whatever they want.
Just as an example, there's a data center in the early stages about 10 miles from my house. The land developer spent a year shopping for a city council that would skip the hearings required by state law and finally found a small exurb willing to break the law. Now the developer is racing to break ground before the lawsuits and restraining orders hit. This isn't the way that a logical society should work.
Is "keeping your mouth shut" dishonesty?
But why shouldn't the possible neighbors of some unpleasant installation protest as much as allowed, and file lawsuits? Neighbors interests have value too, plus we in the USA have a constitutional right to free speech and petition for redress of grievances. The US also has an adversarial legal system. It pays off to file lawsuits if you can afford it.
My conclusion is that "NIMBY" isn't the problem, it's economic incentives and adversarial systems.
grocery stores? They are not comparable to data centers.
I enjoy reminding people the land acquisition history behind building Disney World.