According to Japan Rail Pass official site, Japan Rail Pass that will be exchanged after April 1, 2013 will not cover any JR Highway bus services any more.
- Sapporo – Otaru
- Morioka – Hirosaki
- Tokyo – Nagoya – Kyoto – Osaka (Daytime highway service)
- Tokyo – Nagoya/Kyoto/Osaka (Overnight service “Dream”)
- Osaka – Tsuyama
- Tokyo – Tsukuba center
So if you exchange the pass until March 31, 2013, you still can take a bus in April. I am really disappointed that Overnight bus service will be no longer available for JR Pass user. Especially Tokyo-Osaka/Kyoto overnight transfer is very valuable.
By the way, local bus service will be covered after April 1, 2013. So Lake Towada, Kusatsu Onsen and other bus services will be covered by Japan Rail Pass. But they change the condition without notice. Please make sure that pass cover the service or not before boarding.