On iOS, Cordova has a complex class, CDVLocalStorage which manages backup behavior via the BackupWebStorage flag. It was a little hard to understand the gist of what was going on, so I'm describing the general process of how it works here.... Of course, please note that this information has a limited shelf life due to new releases of Cordova and iOS.
Another note is that if you're building with Xcode, the BackupWebStorage flag is in the config.xml in the Staging area.
Anyways, there are three available values, none, local, and cloud.
When set to none, Cordova does very little and defers to the default iOS behavior which is to store local storage and WebSQL databases in Library/Caches. This is an area which will not be backed up using iCloud.
local has the most complex activity. When set to local, Cordova adds a listener so that when the user exits the app, the databases and local storage will be copied to the Documents/backups directory. This allows a user plugging their device into their computer and running iTunes backup to save those databases/local storage. However, to prevent the iCloud backup from copying these files, the Documents/backups directory is marked with the "do not backup" flag.
When BackupWebStorage is set to cloud, the following is set:
[[NSUserDefaults standardUserDefaults] setBool:YES forKey:@"WebKitStoreWebDataForBackup"];
This flag causes iOS to move the databases/local storage files from Library/Caches to Library/WebKit. Once there, the databases/local storage will be picked up by the iCloud backup.
CDVLocalStorage also creates various Cloud/NoCloud directories but it appears that none of these are ever used.