Machinarium runs at 16:10 so there are only small black bars on the side... Also the game is a bunch of hand drawn vignettes so most scenes edges would have nothing to display but black anyway.
Can you make a 1280x720 patch for handheld mode and can the sharpening filter be reduced or can it only be toggled? The sharpening in this game is definitely too aggressive, but it could use a little sharpening as the image quality is very soft.