Customs is not checking what you have, rather who you are. it occurs when you come back to a US area when your away from a US area.
The process is really just checking your passport that you are who you are, not a biggie.
They do want everyone checked prior to anyone getting off the ship but really they don't wait until every single person is checked, there's always a couple that need to be tracked down. Unless there's some major problem once they get most of the people they will release the ship., but if your someone that didn't clear you will be flagged when you get off thee ship.
Unless your in a rush to get somewhere, wait until the end of the process as you won't have to wait. if you going running there right at the start your going to be waiting on a long line