It is because of the difference in frequency and also honeybee hits its wings whereas pendulum doesnt hit.  it only moves so sound isnt heard
The vibrations produced by a humming bee are quite large as compared to the vibrations of pendulum.

This means the frequency of the sound produced by the wings of humming bee is higher than that of pendulum.

The frequency of the sound of the wings lies in the audible range of human ears, so we can listen it whereas vibrations of pendulum are very low, they are below our audible range i.e. 20 Hz to 20,000 Hz.