Not there
I have heen having the same issue. A random woosh sound at random times. Mine seems similar to when you remove something from your dock. I noticed that two of them are from my two macs being integrated; when one goes to sleep or wakes up, the other makes a woosh noise. But there are other absolutely random woosh noises that started around the time I got my second mac.
I looked through all of the noises in messages, and the woosh noise was not among the ones in use by my messages app. Any other ideas anyone?