Do macOS default preferences ever have breaking changes (the ones we edit with defaults command)? I have a script that uses the defaults command to set a bunch of preferences.

I am curious, do these preferences ever have breaking changes (f.e. when I update macOS), so that I need to modify my script?

If so, where can I find a list of breaking changes?
Like any part of the OS, Apple can change or modify the preference keys. Anecdotally, I can certainly remember people commenting that some keys have been removed, so that setting a particular preference no longer works. 

For instance, Apple changed PMPrintingExpandedStateForPrint to PMPrintingExpandedStateForPrint2 at some point. This is the key that specified whether the print dialog is expanded or simplified.

As mentioned on this site before, Apple does not document many of the available keys; most of which have been found by inquisitive people searching for text strings in executables. So a list of changes seems unlikely.

The defaults write command does not check for validity. So I can add the key IamFabulous -bool true to Preview's plist, and it will sit there doing nothing. Preview will never check for the value of that key. Any 'defunct' key/value will act similarly.