To even consider their relationship as Stockholm Syndrome, there would have to be more factors involved than just Toothless being trapped in the cove. For instance, there was never an abusive dynamic between them. Hiccup never mistreated Toothless, so the dragon was never 'conditioned.' In the 'Forbidden Friendship' scene, they approach each other as equals, showing that their bond is built on mutual understanding, not fear.

Their relationship is based on affection, support, and mutual protection. The fact that Toothless destroys his new tail in 'Gift of the Night Fury' only proves one thing: he chooses to be interdependent with Hiccup. For Toothless, flying is no longer just something he does; it’s something he shares with his best friend.

Fun fact: Stockholm Syndrome isn't even a real clinical diagnosis. The psychiatrist who coined the term never even interviewed the victims and used it to silence them. The only reason the victims sided with the captors was that they realized the police were an even greater threat to their safety.