If the tuner is true-bypass, it's inherent in the design of most true-bypass systems that a pop can occur. (most notably in wah pedals IME) There are workarounds for this, but
AFAIK not every company uses them.
Personally, I don't use my tuner to mute as I have an Ernie Ball Volume Pedal Jr at the end of my signal chain to act as a master mute when I am not playing. (it also functions as my means with which to create volume swells)