If you are able to build such a box, then it will be easy for you to achieve a perfect muting result with no noticable pop sounds at all for most of the microphones.
What you're doing right now, if I understood it correct, is that you turn off the phantom power. For phantom powered microphones this is the wrong way, because this will cause a drastic and therefore hearable voltage drop as the microphone becomes discharged/charged.
The correct way is still to short pin 2 and 3 together. However, in order to achieve a great result, you need to do that twice using a miniature relay with a low contact resistance (e.g. Omron G6A-434P or G6A-234P). Additionally, you may want to solder in a 56 or 100 Ohms resistor (0.1% tolerance) into the both audio signal lines (pin 2 and 3).
The capacitors can usually be omitted, because the most microphones will not cause a noticable pop sound for the small voltage shift which still occurs when shorting the pins together.
This scheme shows how that works, the idea came from
Kirkus:
I built multiple of these boxes (see my article
here) and I can confirm that this way works perfectly: