Rumour has it that this little scene was actually an animation mistake that was kept in because it looked so cool toothless was meant to have his eyes closed throughout the scene.
from the commentary:
"There’s a scene that went by, and I wish we had talked about it as it was happening. But it represents one of those happy accidents that actually does happen once in a while in animation. And it’s a scene where we’re panning from left, or from right to left. We’re moving the camera left. We’re moving up Toothless’s body and there’s a moment where Toothless’s wing is in the foreground and it masks his eye. And the shot had been, I think, originally shown to us with, you know, we pan up the dragon because we’re going to land. The camera’s gonna finish moving on his eye. And we had seen it several times and it worked swell. But then we saw it one time in some other review in the theatre, and it was a mistake that had been made, that had not been corrected. But it was a shot where, as you pan past the dragon’s eye, his eye is closed. And as that wing crosses in front of his eye, it goes to an open eye. It was just one of those ghostly, kind of weird effects that you couldn’t have planned in, one of those things that kind of happened. And we both saw that and loved it and said, ‘Oh, my gosh, you know, go back and make it be like that.’"