Thorin certainly hadn't meant to wake Bilbo up, but there was a small part of him that was glad he had. Spending time with the Hobbit was Thorin's favorite thing to do in this new place. After all, it wasn't something he really had the chance to do back in their own world. So, any chance that they got to try something new, Thorin was always up for it as long as Bilbo was coming along.
Spending so much time with Bilbo also meant that Thorin was getting to learn a lot about the ways of Hobbits. He was very glad about this, because he knew that it wasn't a chance, he would have gotten any other way.
When he saw that Bilbo was shifting on the couch, he made his way over and joined him there. One of the things he had learned about Hobbits was that it really was normal for them to eat more often. Thorin saw nothing wrong with it, and he was more than happy to go out with Bilbo or join him for a meal whenever he was hungry.
"Sure! It would be nice to spend some more time out of the house with you" he replied, being completely genuine with his feelings.