It looks like the pulse repetition rate is about 30 ms. This is based roughly on the 348kohm and 100nF in the 555 circuit. The pulse width is in the region of 200 us. I assume the main oscillator is running at 40 kHz and 40kHz has a cycle time of 25 us.
In a perfect world exactly 8 cycles of 40kHz would be gated by each pulse but, it's not going to work that way. It is likely to be a fractional number of cycles that are gated and this is going to cause a low frequency audible blip that evolves with time as things move into and out of sync.
I don't think it's a problem but you might be better served deriving a pulse from the 40 kHz and gating the 40 kHz to dump an exact number of cycles onto the transducer. You could even arrange it to start at a zero cross. I'm sure this wouldn't produce as much audible noise but then again, on the other hand is it such a big deal. After all, if it performs its main task and the noise isn't annoying then let it be.