Hi Digitan,
That's why the sound of a square wave or any other flat-topped wave (including electric guitar "fuzz") is descibed to sound like a buzzer.
The harmonics are never lower than the fundamental frequency.
Your 25% duty cycle 100Hz signal of course will contain a strong 100Hz fundamental frequency but also many harmonics whose amplitude drops off with their frequency. The harmonics will be 200Hz, 300Hz, 400Hz, 500Hz, 600Hz etc., at multiples of 100Hz all the way up.
With an exact 50% duty cycle the harmonics of a 100Hz square wave will be only 300Hz, 500Hz, 700Hz, 900Hz, 1100Hz etc., only at odd multiples of 100Hz.
Do you like listening to "square waves"? I didn't think the output of an MCU could provide enough current to drive headphones very loud. You could limit the volume by simply connecting a resistor or pot in series with the headphones or as a voltage divider. Headphones don't require the damping of a direct amplifier connection like speakers do.