To clarify, the ferries only carried freight cars on their lower deck. Passengers had to get off their trains at Aomori, board the JNR ferry, and then board their trains at Hakodate to get to their final destinations. It was a tiring process for travelers, as the fastest schdules often involved transfers in the wee hours of the morning, to insure a mid-day arrival in Sapporo.
JNR could have ran direct sleeper services on the ferries, however they were scared stiff of having people drown inside coaches if a ferryboat sank en route (as it happened one particular episode where several ferries sank at the same time during a storm, can't remember the year it happened offhand). Charles Small recounts in "Rails to the Rising Sun" (which I'm reading
yet again as I write now, always fun...

) that JNR used to take down passenger lists in case of an eventuality.
Cheers NB