score:5
1) The link you give refers to a new regional pass covering eastern Honshu and southern Hokkaido, not to the nationwide pass. If you have a nationwide pass, it will be valid.
2) There are no additional fees, but remember that seat reservations are mandatory on all Shinkansens at least between Shin-Hakodate-Hokuto and Morioka (although in your case you will probably just make a reservation all the way to Sendai). You can reserve at a ticket counter of any JR station in Japan at any time, as long as there are available seats. (As of right now, all Shinkansens between Shin-Hakodate-Hokuto and Sendai on March 28 have available seats.) You can also reserve online between Shin-Aomori and Sendai, but not between Shin-Hakodate-Hokuto and Shin-Aomori.