This is how I would like this to play out. Perhaps, Neal is in danger from the WW and somehow being controlled by her. Neal sends the note to Hook so that Hook can save Emma/Henry since Neal perhaps knows about Walsh and the WW plans. Hook cannot let anyone in town know that Neal sent him because they don’t know who the WW is in SB and when she might be eavesdropping. By revealing the truth that he is working with Neal it would put Neal in further danger.
This would allow for some good CaptainFire and also unite the fandom. I don’t know if it will happen this way, but I like to think it’s possible.
YES, for that bit I bolded in particular. JMo has said in recent interviews, when talking about Neal and Hook, that those two have a relationship and mutual respect and whatnot, which frankly makes no sense judging by what we saw of them in S3A, but it WOULD make sense if they’ve been secretly working together in S3B. So that’s the hope I’m clinging to, because my kingdom for some mature, emotional interaction with present day CaptainFire.
Even if Neal’s being held captive by Zelena in SB, it would still make sense to keep it hush hush if he’s the one who sent Hook the message, because if word about that gets out, then there’s the chance that Zelena would find out that Neal’s been working against her, so Hook’s keeping it secret to try and protect Neal. Which, going back to my desire for CaptainFire, would be rather glorious, considering how differently things played out between them in NL back in the day when Hook did the opposite of protecting him from Pan, so YAY character progression.