Why is a Boeing 737 NG engine not completely round in shape? – it seems to be flat at the bottom and round at the top and sides. Earlier Boeing 737 versions (100 and 200) seem to have a more rounded shape.
The engine in question is a CFM56 turbofan engine which is larger than the previous JT8D and thus has less ground clearance. This meant that they needed to flatten the bottom by moving the accessory gearbox to the side from the bottom and shrinking the fan.
To quote Wikipedia:
They also mounted the engine in front of the wing rather than below to get every bit of clearance they could.
You are confusing the shape of the engine with the shape of the nacelle. Axial-compressor jet engines (standard on larger commercial jets) are invariably round and thin1. Engines with a centrifugal compressor are fatter in the middle and will occasionally be lumpy shapes depending on the internal airflow (some engines completely reverse the flow of air through them, sometimes several times2).
Positioning accessories like pumps, starters, generators, control boxes and minor things like mounting brackets are flexible. The engine manufacturer may dictate the position of some things like a gearbox, but if it attaches with a hose it can generally go anywhere the airframe designer wants to put it. The nacelle is then built to contain everything, not produce too much drag, not hit the ground, and preferably not cost too much to make. There's no reason we can't make hexagonal nacelles, we just choose not to.