Speakers humming when used with Raspberry PI 3 and Adafruit MAX 9744 Amp
You didn't show where your PI 3 made its signal ground connection to the main ground rail so I added one in blue.



I'm not saying this is where your humming/pick-up is coming from but I can tell the way you presented your question that you didn't understand about attaching a 0 volt signal return into a power rail that may take amps of current.

The PI 3 signal return should be tied right into the closest 0 volt connection on the MAX9744 as you can i.e. it should share as little of the power rail as possible.