How can I locate and eliminate mysterious water hammer related to humidifier?
Water hammer is caused when flowing water abruptly stops and the change in velocity causes the piping to shake if it's not secured properly.

Look through the pipes you have access to and make sure they're securely fastened. If not, add some more clamps to secure them.

Contact the manufacturer of your humidifier. I'm not sure of the proper terminology but see if they have a replacement for the valve that controls filling the humidifier that closes slowly. My guess is in the morning the humidifier needs to refill itself, opens up the valve and when it's done it closes the valve quickly, causing the water hammer. Might also be another issue that they may know about. 

They also make water hammer arrestors. These devices get installed in the copper lines and absorb the shock to reduce or eliminate water hammer. They will eventually need to be replaced (or if they are the round ones with a rubber bladder may need to be maintained) so install them somewhere accessible. Here's a video on installing a water hammer arrestor.