This saves you and your students time by allowing for single sign-on use of Hypothesis:
The Hypothesis LMS app automatically provisions accounts for all students enrolled in any course using the app. This means that students can navigate to a Hypothesis-enabled reading and begin annotating without ever creating or logging into a separate account. Even better, the entire course roster of students and teachers will all be joined and annotate by default in an automatically-created private Hypothesis group that matches the course in the LMS.
Gradebook integration is a feature planned for the future.
Using Hypothesis in Your Course: Pedagogical Techniques