I am truly sorry for your experience; I hope that no one ever has to go through that. Personally I read fpsndiver's incident report and that has definitely made me a much more thoughtful diver--especially regarding what to bring in terms of safety equipment.
When NCSU goes down to Key Largo on their bi-annual trips right after certifying new divers they go with Ocean Divers. I have been on this trip twice and can say that they are a professional group.
Whenever we originallly get on board before departing the docks they immediately do a roll call--not buddy team numbers or counting heads, but a roll call. They call out every person on the list and you and instructed to stay quiet until they are finished and to answer for yourself and no one else. They then ask if there is anyone on board who they did NOT call (ie anyone who might be there that shouldn't--just because you're not on the roll call doesn't mean that you can't be left behind!)
We had a dive slate with a sign in/sign out chart on it that you were required to initial upon descending along the anchor line and initial after you ascend. Then after we believe everyone is on board we are told to "count off by buddy team"--you are NOT allowed to shout out your number unless your buddy is NEXT TO you--both divers in the buddy team must shout it out at the same time. I believe that this is specifically requested by our NCSU instructors so it might not be an Ocean Divers thing--but I will say that it is in lieu of an Ocean Divers roll call. Occasionally we will use both the roll call AND the buddy team counting method and I believe this is an attempt by our instructors to keep us on our toes...although we are told which method they will use beforehand.
No matter how many times we've been on the boat they give us the safety briefing every time--location of emergency oxygen (right under the ladder), location of life jackets (up front), the head, etc.
I believe in our particular situation we may have as many as 20 divers on each boat at once. However, these are people who we have been in class with for an entire semester so we know each other by name. If someone isn't on board, everyone knows it. When NCSU goes diving with Ocean Divers no one else is on board the boat except for us so it makes it quite easy to know who is on board and who isn't.
For legalities--please note that this is not an "official NCSU endorsement" but is me saying my own personal experience based on who I was diving with at the time.