Here is one study from Rutgers University that analyzes the effectiveness of WeBWorK, and there may be other useful studies or results available on this webpage and this webpage. If you are interested in learning more about the effectiveness of WeBWorK in particular, you should contact Vicki Roth at the University of Rochester.
Ultimately, the most effective homework systems, whether paper or online, get students to actually do their homework and persist until they have achieved mastery of a topic. Anecdotally, after an initial adjustment period, my students who have used WeBWorK actually appreciate that it gives them instantaneous feedback (they love seeing the green bar that says and answer is correct) and allows them as many attempts as they need to achieve mastery (before the due date and on open-ended questions, of course).
There are things that instructors can do to make online homework more effective for students. For instance, instructors should encourage students to keep a homework notebook where they write down complete answers that will be useful for studying later. Also, instructors need to choose online homework questions carefully so that they are relevant, authentic, and on-topic. Online homework questions of low quality that were assembled by someone else are often not aligned with course and do not help students learn (and produce students who are dissatisfied with online homework).