[Update: moved to Harakuku] Owl Village is rather small for an owl cafe - it seems like it would be crowded with more than one set of visitors at a time, so perhaps weekdays are the best time to go. At Y2500 for one hour, it's also on the expensive end of the scale, although there's a small discount if you like the cafe on Facebook.
The amiable staff did give us a thorough and informative personal introduction to the six resident owls (all in Japanese), and we got a chance to hold and pet the most visitor-friendly bird, a small barn owl named Alto, who seemed to enjoy the attention.
The shop also hosts owl-grooming and owl-care seminars (again, all in Japanese), and sometimes the staff members take the owls out for walks in the neighborhood.