I've owned almost every iPad since their creation and unless you manually select to fill the YouTube videos, effectively cutting off all the sides, then what you're saying is not true. Maybe you have the YouTube setting to automatically fill (zoom to fill screen in settings) but that's not native resolution for any iPad.
As I said every single iPad will have letterboxing in YouTube except for those made specifically for an iPad resolution which are few and far between. Maybe check your YouTube settings.
Here's an example of a video shot specifically for the iPad 12.9" 4:3 ratio: