Do the lights dim in your neighborhood when DH switches on the home theater? :-)

Seriously, that subwoofer would have to be pumping out some serious bass to do that to any floor which was installed properly. If you want to rule out the subwoofer as the cause, you can mount it on something which will "decouple" it from other hard surfaces. Audio places sell synthetic "feet" you can use; you also could put a pillow or towel or yoga pad under the subwoofer. You'll lose some of the "thump" but it at least will confirm or deny that the subwoofer is damaging the floor.

It is more likely that the weight of people in the kitchen are flexing the floor and causing it to crack. The floor may not be stiff enough. People walking in the kitchen are going to cause more vibration and flex that a subwoofer on a lower floor.

Yup. Too much deflection in the granite installation. It has nothing to do with subwoofer vibration.