What kind of onboard security are you talking about? The ferry is a very safe place, lots of families with kids running about, backpackers, couples with no kids and groups of singletons. The doors to the decks tend to be heavy affairs (to stop them blowing in and out) so it's highly unlikely that your kids will be able to get out on deck without you.
Your cabin is allocated to you when you book, then when you board you go straight to the cabin where the door will be open and the key will be on one of the bunks. So you can lock the door and you're as secure as you'd be in a hotel. Most people go to bed reasonably early as there is usually a lot of driving to be done when you land in France.
If you've read about fights breaking out between football fans on the ferries to Scotland or England, you can forget about that carry-on, the ferry to France is a completely different environment.