True bypass switch pop is almost always caused by a small amount of DC voltage buildup on the pedal input or output. This could be caused by voltage leaking out of the input or output of the pedal. When you switch from bypass to effect mode, the pop is caused by the audio signal "meeting" the voltage present on the circuit input or output.
This is usually either caused by DC leaking out of the circuit input or output (from bad circuit design or from a leaky input or output cap) or it can even be caused by static electricity. True bypass circuit designs usually include pull down resistors on the circuit input and output to combat this (typically 1-2 meg in the input and 100k on the output). The function of these resistors is to allow any DC voltage present to drain away to ground without dumping too much audio signal to ground. This system fails when the source of the voltage is too great for the pull down resistor to effectively dump it to ground.
Here is the best article I've read on the subject:
https://www.mrblackpedals.com/blogs/straight-jive/6629778-what-really-causes-switch-pop