Why did Summer B wake up just as the ship was about to sink?
The 'ship' was actually their cyrogenic unit that had launched to the surface (from deep within the ocean) after its computer had deemed the circumstances right to awaken its inhabitants. This is why they woke up just as the ship reached the surface and appeared to be 'sinking' due to the storm.
And shouldn't the Government have to inform the participants in the Seven Seeds project that they are going to be cryogenically frozen?
It's mentioned in the various Apocalyptic Logs that in the immediate years after impact, contact between the shelters and manned Fuji facilities were eventually lost. This could simply be the result of faulty equipment or the communication lines decaying. But it's never stated outright that the other Japanese shelters were destroyed, leaving the possibility that there might still be a few out there that are actually surviving.
According to Mark's journal, the Ryugyu shelter was designed to have enough food supplies to last three years. Take a guess how long said shelter lasted until everyone in it died.