We don’t know that he is on Hook’s ship at all. That’s someone’s cracktheory, that a rat got on board. But so far as we know Smee is still a rat in SB and probably will be for the foreseeable future.
As to being a double agent: double agent for whom? For Hook? For PP? I don’t think I understand what you’re getting at. Wouldn’t be Hook, he didn’t know him. For PP? Eh. What does PP get out of it? Had Rumple been able to use the bean, he would have gotten to a Land Without Magic or NL and that would have blown PP’s plans. I really think Smee is just an independent guy until he meets Hook.
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"He was a lot of things to me" "The only conclusion was love"