I think the wording in the Documentation could be a bit clearer on this. It talks about two different settings in the same paragraphs. I think it should explain them separately and not talk about one type in the others to avoid this confusion.
There are two notions of ‘Hidden’:
Element Visibility & Locking
Clicking the eye icon for elements in the element list will Hide the elements on the scene and they are also not included in the exported document.
Hiding elements this way is intended to not include them in the final export but to keep them available in the project for your use.
Opacity & Display
Setting the Display value to ‘Hidden’ in the property Inspector for an element will set the CSS Layout property display:none on that element; this is an animatable property. Use the ‘display’ option during animations to instantly hide or show an element on the scene.
When elements are hidden this way they are included in the export and will be hidden on the scene but they will only be interactive when they become visible.