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.