winuae uses rawinput, normal windows injection methods won't work. (I don't know what autohotkey needs to do in this case)
You can also use 3.3.0+ gameports panel custom mapping. It does exact same thing, map key to Amiga joystick/mouse. (But I just remembered that it has a bug that causes mappings to be lost, you need 3.4.0 beta..)
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