DCAU!Jason would find out from Mechanima that Atomight has been missing for several weeks. As for what happens - there is already chaos happening in the prison with them breaking Jason and Roy out. Nothing drastic would happen when the cell opens.

IS he Atomight?
It is Atomight!

Do they get clear of the island with all present and accounted for?
Yes. Atomight will be very tired and unable to assist. He'll need someone to carry him off island.

Does Atomight need to be stowed somewhere until morning so he can sun himself back to full power?
He will need to be stowed somewhere, but he will let them know they can drop him off with Mechanima if they don't have somewhere safe for him. He will be immensely grateful for the help