There are already 16 daily round trip ferry service between Aomori and Hakodate by two ferry companies carrying cars and trucks where journey takes 3 hr. 40 min. Also, there is ferry service between Hakodate and Oma, Aomori where Oma is located at northern tip of Shimokita Peninsula and the journey is 1 hr. and 30 minutes.

Beside that there are 12 weekly ferry trips between Ooarai, Ibaraki and Tomakomai, Hokkaido which is serving truck/car demand between Greater Tokyo area and Hokkaido. There used to be a ferry service from Tokyo Ferry Terminal which is near Odaiba to Tomakomai but the service terminated more than few years ago. Also there are ferry services from Hachinohe, Aomori and Sendai to Tomakomai.

Over at Sea of Japan side, it is not daily service, but service from Akita, Niigata, Tsugaru (Fukui), and Maizuri (Kyoto) to Tomakomai. Yes, Kyoto is not just the city of Kyoto with temples. Kyoto extends all the way to Sea of Japan.

Anyway, there are already several established ferry services carrying cars and trucks between Honshu and Hokkaido. If JR wants to tap into that market by doing auto train between Aomori and Hakodate, then how much demand JR can capture away from existing ferry services?

Also there is JR inside logistic issues. Seikan Tunnel belongs to JR Hokkaido, not JR East, hence newly opened Hokkaido Shinkansen belongs to JR Hokkaido. Then there is separate JR Freight division which operates freight trains all over Japan. JR Hokkaido and JR East operate passenger trains only. There used to be sleeper train with dining car running between Ueno (Tokyo) and Sapporo (Hokutosei and Cassiopeia) and Osaka and Sapporo (Twilight Express) where all these sleeper trains terminated operation before inauguration of Hokkaido Shinkansen.

Seikan Tunnel was re-fitted for dual Shinkansen and regular train for service inauguration of Hokkaido Shinkansen. Now Seikan Tunnel has new electric and other train specifications for trains running through the tunnel. JR Freight has ordered new electric engines dedicated for Seikan Tunnel to pull freight cars. If JR wanted to continue sleeper train service between Honshu and Hokkaido then JR Hokkaido had to order brand new electric engine dedicated to Seikan Tunnel only to pull two or three sleeper trains passing through the tunnel. It did not make JR Hokkaido financial sense to do that, when JR Hokkaido knew that new Hokkaido Shinkansen will be bleeding US$42.5 million annually in red.

Then Auto Train will be combination of freight and passenger cars. There are big logistics problems need to be worked out between JR Freight and JR Hokkaido. Also need to make new stations to load and unload cars and who will build that, JR Freight or JR Hokkaido? With Hokkaido Shinkansen bleeding red big time, can JR Freight and JR Hokkaido establish fares for Auto Train which is competitive with existing ferry service?

There is Auto Train example at English Channel tunnel and I am sure JR has studied that example. But with specific situation of Hokkaido and Honshu car transport demand, I think JR Hokkaido has decided that it is not what they want to do at this moment.

Alright, a lot of train geek talk.

P.S.
Found the number for Tokyo-Fukuoka. Shinkansen takes about 8-9% passenger traffic between Tokyo-Fukuoka, where airplane takes 91-92% of passenger traffic between Tokyo-Fukuoka. Shinkansen is winning on Tokyo-Osaka, Tokyo-Okayama, Tokyo-Hiroshima, and Osaka-Fukuoka.

However, passenger demand between Sapporo/Hakodate-Morioka/Sendai is so low compare with above city pairs that JR Hokkaido is not in same situation as JR West and JR Kyushu when it comes to Shinkansen.