I think it's really important for the adults to talk about their expectations before they go. When DH and I took our kids the first time, they were 1.5, 4, and 7 years old. We decided going in that doing things together was the priority. We skipped headliners that the kids were too short for.
If they want to be able to do Space, etc, they need to have a child swap plan or whatever, but I think talking about it ahead of time is worth the time.
I am a huge proponent of the midday break, but with only one day, they might not be willing to sacrifice the time.
Budget permitting, I recommend the Crystal Palace for as late a breakfast as you can get and treat it as lunch. Lots of great character interaction and good food that kids that age will eat. Everyone will enjoy a break-- especially if they've been up and at 'em for for hours. Often families with little ones can make it to rope drop pretty easily since young children are usually early risers.
I hope they have a wonderful time.