Yes, relying on Hyperdia can lead you into some odd routings. When I was planning my last train trips (Tokyo to the San'In Coast to Hakata and then Beetle hydrofoil to Korea in one year and Hiroshima to a circle tour of Shikoku to Tokyo in another year), Hyperdia suggested some routes that made me pause and think, "I suppose one could go that way, but it would require a lot of backtracking"

Fortunately, I know Japanese geography well enough to know which routes make sense.

I highly recommend using Hyperdia in conjunction with a map of Japan, which would reveal, for instance, that you have to go through Hakata to reach Kagoshima.