Bearing Buddies do work great at greasing bearings easily and helps to push the old grease out of the bearings especially when you have a boat trailer that goes into the water.
You can easily grease the bearings again and push any potential water out of the bearings through the use of bearing buddies.
Bearing Buddies work by pumping grease into the center of the hub all the way back to the wheel bearing grease seal.
Then it will fill the cavity inside the wheel bearing hub and continue to the inner wheel bearing.
So yes the inner bearing will be greased with the use of the bearing buddy.