At the summit ridge between Nantai and Nyotai peaks, a small traditional teahouse sells hot tea, amazake (a mild sweet fermented rice drink), and simple snacks. After two hours on the trail, it is exactly what you want.
The teahouse commands the same panoramic view as the rest of the summit — the Kanto Plain stretching south toward Tokyo, and on clear autumn or winter days, Mount Fuji on the horizon. Sitting down with a cup of green tea after the climb and looking out over the plain is one of the quieter pleasures of a day in Tsukuba. The prices are higher than they would be at the base of the mountain, as is traditional in Japan for summit refreshments, but not unreasonably so.
Opening times depend on the season and weather. In summer the teahouse may open early and close by mid-afternoon; in winter it is less reliably staffed. Do not count on it for a hot meal — bring your own provisions if you will be spending several hours on the mountain.