Any vibrating body will produce sound unless it is in vacuum, in which case off course there would not be any sound, since sound requires a medium to propagate. When a pendulum swings from side to side it will obviously collide with the air particles in the air and they might vibrate a bit too producing some sound. But we don't hear it.
The vibrations do reach our ears, but because we can only hear from 20 Hz to 20,000 Hz , we don't hear it. The frequency of sound produced due to vibrations of seconds pendulum is 0.5 Hz which is infrasonic sound.
Hence, the seconds pendulum is not heard.