@zing Yes, after each test, I did a factory reset from menu.

Thanks to your link I found something that changes on \SHARE\system.emulationstation\es_input.cfg

I realized that after configuring correctly:
config.jpg

This was changed on es_input.cfg:
ps3-input.jpg

<input name="r2" type="axis" id="5" value="-1" code="5" /> <input name="l2" type="axis" id="2" value="-1" code="2" />

The solution was change the values of L2/R2 from before the controller config. Restart and Kodi stop muting when pressing L2.

Don't know why configuring changes those values, I did it many times so I'm sure I pressed the correct buttons every time.

Thanks a lot @zing for the patience and helping me. I hope this helps anyone with this problem too.