I believe hypertext reading is deeper, and that this is obvious, almost true by definition. Non-hypertext reading is exactly 1 layer deep. Hypertext lets the reader go deeper. Literally. You can zoom in on any topic.

It has deeper structure, but that is not necessarily user-friendly. A great textbook will have different levels of explanation, an author-designed depth-diving experience. Depending on author, material, you and the local wikipedia quality that might be a better or worse learning experience.

Hypertext reading lets you find your own connections, and lets you find background knowledge that would otherwise simply be edited out of a book.

Yep, definitely a benefit, but not without a trade-off. Often a good author will set you up with connections better than you can.