What you missed in your list, is the couple of hours hanging about in the airport each end.
We took the overnight ferry to Holland a couple of years ago, and it was great, but not sure how it would be with 3 little ones, ours were 6 & 7 at the time. The worst bit of that trip was the 4 and a half hours in the car to and from the ferry terminal.
If it was me, I would be tempted to fly, because my eldest gets travel sick if he watches the tv or plays on his ds (unless we are on motorway and then he is okay for short periods) so we would probably not drive for so long again. If your kids are fine in the car, then you do have the advantage of having your owns things avaialble to you for the journey and you can stop and start when you like.
In any case, I would get your son a new car seat if his is not comfy for him regardless of what you do for the holiday - you only get one back!
I wouldn't hestitate to take our 2 on the ferry again, as long as it was closer to where we live, but being in Scotland, our options are a bit limited on that score!!!