I ride Honda CD-100 SS, a 100cc motorcycle.
Does increasing the wattage of the headlight bulb affect the mileage(fuel efficiency) of the motorcycle? If it does please explain how.
Not by any amount you can measure, no. The power consumed by the bulbs are such a small fraction of the total that you would not notice it, unless you are adding multiple spotlights or going all retro-mod, maybe, like this pic from the Telegraph:
If you're not increasing the load on the engine then mileage(fuel-efficiency) remains unaffected.
Coming to your question, when you replace say a 35W(12v) bulb with 50W(12v) then new bulb will not glow to its full capacity.
However, if you rewind the stator-coil to produce more current then technically more load is on the engine. This load from stator(magneto) will always be there whenever engine is on.