I went to Vietnam in October 2011 and the cruise in Halong Bay was a fantastic part of the holiday.
It is quite a long drive to the junk from Hanoi (I think it was about 5 hours) but it was really worth it. We arrived at the boat in time to be served a very good seafood lunch and there was an optional trip in the afternoon, that I did not take. We also had dinner and breakfast on the boat.
There were 35 in our party so we had 2 junks. In the evenings these were lashed together and people could transfer from one boat to the other if they wanted to.
Your main suitcase remains on the coach overnight so you need to take a small bag for the things you need. In the morning you drive straight to Hanoi airport. Most people opened their suitcases at the airport before checking in to avoid taking their toiletries (liquids) as carryon luggage.
As with rooms in the hotels I think some people had better cabins than others and it is just the luck of the draw. I would describe my cabin as adequate (all cabins had private facilities). This was not a problem as I spent very little time in the cabin. The floor in the shower room did get very slippery. I think that some of the cabins were provided with rubber foot ware but there were none in mine. I suggest you take your own, just in case.
The main thing you will need is your camera!
Please ask again if there is anything else you would like to know.